There are two major differences, the ending and the POV of the stories.
In the book, everything is told from Bruno’s perspective and he really knows nothing about the horrors of the camps and the Holocaust. In the movie, its told by a 3rd person POV.
In the ending of the book, no one knows what happened to Bruno. Elsa and Gretel head home but weeks later they find Bruno’s clothes near the camp. In the movie, Gretel and Elsa have a huge search through the camp to try and find Bruno. At the end they find his clothes and a hole dug under the fence, that’s how they found out he died.
There were a lot of other changes. One was, in the movie Lieutenant Kotler was sent away because Brunos dad found out his father fled the country at the start of the war, making him potential unfaithful to the Nazis. In the book, it was implied that Elsa was having an affair with Kotler. Bruno’s dad found out about the affair and sent him away.