Andre Young, 21, is charged with injury to a child-serious bodily injury. The child's 21-year-old mother, Jasmine Jones, was arrested when she surrendered to authorities on Dec. 10.
Jones' son Jacion was pronounced dead Nov. 8 after paramedics were called to their west Houston apartment.
"It's probably one of one of the worst cases we've seen," said Houston Police Sgt. Chris Hassig.
The beating that toddler took, investigators say, was not a one-time thing. They discovered his injuries were in various stages of healing. There was bruising to his buttocks, back, abdomen, pelvis and head.
Investigators say Jacion had previously been removed from his mother's custody. They told Eyewitness News she claimed he sustained second-degree burns while turning on hot water in the shower.
Jacion was removed from the home for 18 months and had just been returned to her in October. Investigators say she did not face criminal charges in that case.
Following Jacion's death, a 10-month-old girl who was also living at that apartment was removed by CPS.