1. The hab's airlock was the size of a telephone booth in the book. In the movie is a large tunnel made of hab canvas.
2. Mark Watney operating on himself to remove a piece of antenna was far more graphic in the movie than in the book.
3. Venkat Kapoor's name and ethnicity got changed in the movie. In the book he is Hindu. In the movie his name is Vincent Kapoor and he is half Hindu, half African American, so Chiwitel Ejiofor could play the part.
3. In the book Watney uses the hab's entire floor, the cots, and even the desks for farming, as well as some canvas extensions. In the movie he only uses the center of the hab.
4. Several great lines in the book such as "I'm pretty much fucked", "my asshole is doing as much as my brain to keep me alive" and Watney's "fuck you" to Mars were left out. The movie does add one really good line that wasn't in the book: "I'm going to have to science the shit out of this."
5. There were two rovers in the book and one was used by Watney as a trailer. In the movie only one rover is used and an actual trailer.
6. In the book the helmets for the EVA suits had a radiation shield that didn't allow Watney's face to be seen. In the movie you can always see his face.
7. Thus, when Watney takes his picture with the thumbs up you can't see his face. AND, in the book he's holding a sign that says "Eeeeey". In the movie Watney only does the thumbs up.
8. In the book the rover has an airlock. In the movie it doesn't.
9. In the book the Pathfinder probe breaks down after Watney accidentally fries its circuits, so he communicates with NASA by using rocks to form Morse code messages that Mars satellites can read. In the movie, Watney takes Pathfinder all the way to the Ares IV site and Morse is never used.
10. In the book Watney has to figure out how to navigate the rover around a sand storm. That sand storm is never shown in the movie.
11. In the book Watney makes a jacuzzi in the hab to treat his back after he's injured working on the rover. That is left out in the movie.
12. In the book both rovers roll over when Watney drives over a sand trap. rover 1 is turned to its side and rover 2 ends up completely upside down. This never happens in the movie.
13. Johanssen telling his father in the book about the cannibalism contingency plan is left out, along with Martinez's joke to Johanssen asking her who would she eat first.
14. In the book Annie Montrose swears and is pissed most of the time. In the movie she is only slightly annoying.
15. In the book Mindy Park is Korean. In the movie she's American. Although, to be fair, we only know that because Andy Weir said it in an interview.
16. HOWEVER, in the book Mindy Park starts being meek and afraid and ends up being a smartass and talking back to Venkat Kapoor. In the movie she always stays the same.
17. In the book Watney comments that he's close to the Opportunity probe and he could reach it, but ultimately decides not to do it. The movie omits this altogether.
18. In the book, Watney makes a "room" out of hab canvas that he attaches to the rover's airlock so he can sleep laying down. The movie doesn't have that canvas room.
19. In the book Watney sleeps in the rover after he realizes there's too much oxygen in the hab when he was turning hidrazine into water. In the movie he doesn't.
20. In the book, Chris Beck gets Watney directly from the Ares 4 MAV. In the movie, obviously so Jessica Chastain can look more heroic, Commander Lewis gets Watney.
21. In the book Watney suggests that in order to cover the gap in distance between the MAV and Hermes he could make a hole in his space suit and fly like Iron Man, but Lewis vetoes that idea. In the movie, Watney makes the hole and flies towards commander Lewis.
22. Lewis's significant other shows her an ABBA 8-track from 1976 that will be added to their disco collection. In the movie he shows Lewis an LP of ABBA's greatest hits.
23. The book ends after Watney is safely inside the Hermes. The movie adds an epilogue in which Watney teaches a class on how to be an astronaut while the rest of the characters -including a Johanssen who just gave birth to Beck's kid- watch the launch of the Ares V mission, piloted by Rick Martinez.
24. The book makes clear that the Chinese agreed to let NASA use their booster for sending supplies to the Hermes for political gain, so a Chinese astronaut can go to Mars in the next mission. The movie makes it look as though they did it for humanitarian reasons.
25. Watney emails each one of the Ares III crew individually, telling them personal messages, including one message to Beck telling him to tell Johanssen how he feels about her. The movie only shows one email to Commander Lewis.
26. The book reveals Beck and Johanssen are having sex as a surprise later in the plot. The movie suggests they have a relationship in a more obvious and less racy fashion.
27. In the book, Watney turns off his microphone when he gets pulled out of the MAV by Beck because he was screaming in pain due to the fact that he broke a rib during the launch. In the movie Watney simply says he broke a rib.
28. After the airlock explodes in the hab with Watney inside, the book shows Watney having a nervous breakdown and even saying he will just commit suicide. Then, after he calms down, he fixes his helmet and a crack in the airlock with resine and material from his EVA suit by cutting an arm off the suit. In the movie he only fixes his helmet with duct tape and the suit is left intact. Also, in the book Watney rolls the airlock closer to the rover so he doesn't lose oxygen. In the movie he goes straight to the hab to look at the damage. That must be some duct tape.
29. The sand storm at the beginning of the book and the movie happens only once in the book. In the movie it happens again after Watney reaches the hab. The problem with this is the storm was not possible to begin with. Andy Weir put it as a plot device because it was a man versus nature story and he wanted nature "to have the first punch", but he has always acknowledged that due to the virtually non-existent atmosphere in Mars, sand storms are only felt as a gentle breeze and the sand storm was a liberty he took with the actual science just to make things more dramatic.
30. In the book Watney makes jokes about the crappy 1970's TV shows Lewis has in her computer, including Three's Company and The Dukes of Hazzard. Happy Days is only mentioned as a passing reference to justify Watney's "Eeeey" photo. In the movie, Watney is seen watching an episode of Happy Days and the other shows are not even mentioned.
31. The Aquaman joke in the book was left out of the movie and put in the promotional materials.
32. The "help each other out" speech at the end of the book was left out of the movie and put in the teaser trailer.
33. In the book Watney has a discussion with NASA in which he warns them not to blame anyone for his situation, or else he will publicly deny it, because, NASA suggests, the government will want somebody to blame. This discussion never happens in the movie.
34. In order to keep the movie PG-13, the "hey boobies (.Y.)" joke from the book gets censored.
35. All of the "Watney Report" CNN clips from the book are not shown in the movie. Only one news clip is shown briefly explaining why the first supply probe failed after launch.
36. In the book, Watney writes the ASCII messages he gets from NASA through Pathfinder in the sand. In the movie he writes them with a pencil on paper.
37. In the movie, Watney takes the packaged excrement from the crew to make fertilizer for his potato crops. In the book he uses his own. (UPDATE: Watney does use the crew's poop as fertilizer in the book. The part I can't remember nor find in the book is Watney smelling Johanssen's poop, though.)
38. Speaking about excrement, in the book Watney defecates and urinates into a plastic box in the rover during his trip to the Ares IV site and then dumps it outside along the way. He never does that in the movie.
39. In the book Watney never uses ketchup for his potatoes, as he does in the movie. In fact, he eats them raw until he realizes he can cook them and then keep them outside the hab to freeze.
40. The Iris "gay probe" joke from the book was left out in the movie.