The French actress, who plays femme fatale Sévérine in the latest 007 movie, will be the second Bond girl to team with Malick after Olga Kurylenko worked with the director on To The Wonder.
Marlohe will shoot her role in the untitled drama concurrently with the Skyfall publicity tour, says The Hollywood Reporter.
Christian Bale, Cate Blanchett, Michael Fassbender, Ryan Gosling, Rooney Mara and Natalie Portman are already onboard the cast for the film, which is currently shooting in Austin, Texas.
The film's story follows a pair of overlapping love triangles set against the backdrop of the music industry.
Skyfall is showing in UK cinemas now and will open in the US on November 9.
Watch Marlohe and the stars of Skyfall talk to Digital Spy at the film's world premiere: