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Justin Ross Harris, 33, also faces two counts of felony murder for the June 18 death. The eight-count indictment by a Cobb County grand jury includes charges of child cruelty and a criminal charge involving sexual exploitation of a child.
The death penalty is possible in case of conviction, said Cobb County District Attorney Vic Reynolds, who will decide whether to seek that sentence in the next two to three weeks.
"The evidence in this case has led us to this point today," he said in a statement.
The case of the suburban Atlanta father, who has been jailed since his son's death, has drawn attention to a tragic cause of death in children.
So far this year, 26 children have died of vehicle-related heat strokes in the United States, according to KidAndCars.org. On average, the group sees 38 such deaths each year. Although parents typically face criminal charges in about half the deaths, the group said felony murder charges were unusual.
"We've seen some pretty extreme charges this year," said Amber Rollins, director of the nonprofit organization, based in Kansas City, Missouri.
The indictment said Harris acted "with malice aforethought" when he placed his toddler in a car seat and left him in a sport utility vehicle on a day when the temperature was in the 90s F.
Harris told police he forgot to drop his son, Cooper, off at his daycare center on his way to work and only discovered the child after he left the office that afternoon.
Prosecutors contended that Harris deliberately left Cooper in the car because he wanted to live a child-free life.
Harris' attorney, Maddox Kilgore, has argued there is no proof his client knowingly left the child in the car.
In July, a judge ordered Harris to remain jailed without bond after hearing evidence he exchanged nude photographs with women other than his wife while he was at work and his son was dying in the car.
Investigators testified that Harris did Internet research on living child-free and how to survive in prison before his son's death. He was having marital and work problems, investigators said.
Harris' wife, Leanna, was interviewed by authorities but has not been charged in the case.