Those who have both seen the movie and read the book say that the movie is nearly identical to the book. There are some minor changes to details that don't affect the story, e.g., the professor and his wife are older in the book than in the movie. Eleanor's homelessness and guilt over her mother's death aren't revealed until near the end of the book, and her eventual death is a deliberate suicide, not caused by an invisible force. The movie also changes the character of the Professor's wife. In the book, she is rude, self-absorbed, and overbearing, as well as being a wide-eyed believer and uses a planchette to contact the "spirits", getting information that is completely wrong. She believes she knows way more about the supernatural than the Professor and chastises him for his slow deliberate "scientific" method. Professor Montague of the novel becomes Markway in the film, Eleanor Vance's last name becomes Lance in the film. The movie leaves out a few scenes, such as a small occurrence involving a ghoulish nursery rhyme. Again, this doesn't affect the story. One mentionable deviation is that Nell's infatuation with the professor is not in the book, and Nell actually comes on to Luke at one point in the book. One interesting difference is the focus; the book is about the haunting of the house, while the movie focuses more on Nell's nervous breakdown, and raising the question of whether it's really happening, is all in her imagination, or the result of latent psychic powers running wild.
Some supernatural events in the book are not depicted in the movie, as follows:
(1) At one point, Theo returns to her room to find her clothes thrown about, trampled, and smeared with what appears to be red paint or blood, and on the walls and ceiling is written "Eleanor come home Eleanor." They close the room off and Theo wears Nell's clothing, but a few days later Mrs. Montague enters the room and finds nothing wrong, and Theo's clothes neatly put away.
(2) Mrs. Montague's planchette, which gives a number of nonsense messages about ghostly nuns and hidden treasure (a reflection of her romantic and gullible notions of the haunting), but then has a series of messages about "Eleanor Nellie Nell Nell" with repeated references to "home", "lost", and "mother".
(3) One scene of the door being pressed against in Theo's room is noted by complete silence; even Eleanor and Theo cannot hear each other talk. Another time, Theo and Nell fall asleep with a light on, but Nell is wakened by voices and the room is pitch dark; it's not until she screams that suddenly the light is on again. There are other times when characters call to one another but cannot hear each other or hear something else entirely.
(4) Theo and Nell go for a walk outside, and suddenly everything appears in "negative", with a black sky and white trees. They see a ghostly family on a picnic, beckoning them to join, but Theo looks behind her and screams for Eleanor to run and not look back. As soon as they start running for the house everything is normal again. Theo never describes what she saw, but it is clear it was something she found terrifying.
(5) During the next-to-last night, when it sounds like the house is falling apart, Mrs. Montague (asleep in the nursery) and her friend Arthur (asleep elsewhere) don't hear what the others do; Mrs. Montague only complains that her room is stuffy, and Arthur complains of a branch tapping at the window.
(6) Nell, Theo, and Luke take a walk outside, and at one point Nell walks ahead and assumes the others are right behind her. She turns and realizes they're nowhere near, and she sees the grass being moved by an invisible presence, which passes her, crosses a stream, and continues on.
(7) During Nell's last day in the house, she hears a phantom voice singing outside, and in her final insanity runs around the house, led by calls from a phantom voice that sounds like her mother. It is unclear if these voices (and some other events) are really happening or are symptoms of Nell's crumbling sanity.