In the movie, he is already the Commissioner of the Gotham City Police Department at the beginning of the story. This is an established fact from the very beginning of the film.
It's possible you are thinking of the Batman: Arkham video game series. In those games, Gordon is initially a Captain but rises to the position of Commissioner over the course of the story.
However, in the new Batman movies, Gordon is firmly established as the Commissioner, working alongside Batman to clean up the crime-ridden Gotham.