Carlotta Pierce is charged with assault and endangering the welfare of a child.
The body of her daughter, Marchella, was found in their Bedford-Stuyvesant home Thursday.
The girl had medical problems since birth and was just 15 pounds when she died.
The medical examiner found marks on the child's wrists and ankles that were consistent with being tied up.
Prosecutors say the child had been force-fed sleeping pills.