The main literature prize, le Grand Prix de litterature Henri Gal worth €40,000 euros, will go to Khadra, whose real name is Mohammed Moulessehoul, the academy said in a statement.
Khadra, who wrote under his female pseudonym to avoid military censorship, only revealed his true identity in 2001. He is best known for two novels set in Afghanistan under the Taliban, The Swallows of Kabul (2006) and The Attack (2008).
Moroccan Abdellatif Laabi will be awarded a prize worth €22,500, it said.
Other reward recipients include philosopher and novelist Jean-Bernard Pontalis, botanist Francis Halle, poet Franck Venaille and cinematographer Daniele Thompson.