Sean Arlandis Alexander initially was charged with felony child abuse, but the charge was upgraded Wednesday after the toddler died.
Ridgeland police Lt. Brian Myers said Alexander is being held without bond at the Madison County Detention Center pending his initial appearance in Ridgeland Municipal Court.
Authorities say the girl was injured Sunday.
Police Chief Jimmy Houston told The Clarion-Ledger that the toddler had bruising on the rib cage and there was bleeding from the brain.
It was not immediately known whether Alexander has an attorney.