Investigators believe the boy was shot with pellet guns, pepper-sprayed and was handcuffed to a coat rack in a closet.
The couple is being held in the Oconee County Jail. Each were charged with a single count of first-degree cruelty to children.
Authorities said its likely they could face additional charges.
Athens-Clarke Police opened an investigation Monday to determine if the boy had also been abused at a local motel.
The boy is now living with a foster family.