Police found the boy a few hours after he was reported missing from his home on Bayou Homes Drive in Galveston last month.
Officers say the boy claimed he didn't want to be locked in his room.
According to court documents, police found an eight-by-six-foot box in the home that the boy's father admitted was the child's room. Inside was a small blanket, socks and a book, records state.
They also found evidence of child pornography.
No charges have been filed, but the investigation is ongoing.