The Academy of Motion Picture Arts and Sciences will give the trophy to the filmmaker "in recognition of a visionary and powerful experience in storytelling," reported Variety.
The award will be presented at the ninth annual Governors Awards on November 11.
"Inarritu and cinematographer Emmanuel Lubezki have opened for us new doors of cinematic perception. Inarritu's multimedia art and cinema experience is a deeply emotional and physically immersive venture into the world of migrants crossing the desert of the American southwest in early dawn light.
"Carne y Arena" is currently on display at the Los Angeles County Museum of Art.
The Academy rarely extends special awards. The last time any such accolade was presented was in 1996, when Pixar's "Toy Story" received a special achievement award from the organisation.
Also set to be honoured at the Academy's Governors Awards are filmmakers Charles Burnett and Agnes Varda, cinematographer Owen Roizman, and actor Donald Sutherland.