Peter David will bring the Marvel Comics title to the new medium, starting with the 'Gifted' story arc.
The Avengers director Whedon worked on Astonishing X-Men in collaboration with artist John Cassaday between 2004 and 2008. His run spanned issues #1 to #24, paving the way for Warren Ellis to take over as writer.
David is best known for his 12-year run on The Incredible Hulk. He has prior experience adapting work for new mediums, having brought Stephen King's Dark Tower series to comics.
Marvel has previously sanctioned the release of prose novels based on its Civil War event and Amazing Spider-Man title.
Astonishing X-Men: Gifted will be released on September 5.