Producers of the multimillion-dollar film have signed a deal, said to be worth £100,000, to use the building as a double for London's Westminster Abbey.
Production crews will be in Lincoln for two weeks in the summer. Filming will centre around the Chapter House, Cloisters and Nave.
Cathedral chief executive Roy Bentham said Lincoln and another unnamed British cathedral have been chosen for the film, which is expected to open next May.
He said: "With (book) sales worldwide in excess of 20 million, the film is sure to generate an enormous amount of interest in the cathedral and the city of Lincoln.
"Filming is due to take place this summer and may involve some disruption to visitors, although every effort will be made to keep this to a minimum."
Alec Knight, the Dean of Lincoln, added: "The book is an exciting story and I hope the film is a success.
"To me, as a Christian, there are aspects of the book that make no sense at all, but at least the film will ensure that our faith is discussed as a live issue.
"If people want to find out the truth, we shall be happy to help them."