The Atlantic County Prosecutor's Office said the indictment was made Tuesday by a grand jury that accused the couple of child endangerment.
Marty Small also was charged with assault and making terroristic threats.
Prosecutors said both parents hit and emotionally abused the girl, who was 15 to 16 years old, on multiple occasions in December and January.
The Smalls have asserted their innocence, calling the situation a "private family issue." Neither Marty Small nor the attorney representing the couple immediately responded to messages seeking comment Wednesday.
It could not immediately be determined if the girl is still living at home with her parents.
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Prosecutors said that on Jan. 13, 2024, Marty Small Sr. hit his daughter multiple times in the head with a broom, causing her to lose consciousness.
Ten days earlier, they said, Small engaged in an argument with his daughter, grabbing her head and throwing her to the ground, and threatening to throw her down a flight of stairs. He threatened to "smack the weave out" of her head during the incident, according to prosecutors.
The 50-year-old Democratic mayor also is accused of punching his daughter repeatedly in the legs, causing bruising.
La'Quetta Small, 47, is accused of punching her daughter multiple times on the chest, leaving bruising. In another alleged incident, she is accused of dragging her daughter by the hair and striking her with a belt on her shoulders, leaving marks.
In yet another incident, La'Quetta Small is accused of punching her daughter in the mouth during an argument.
The indictment of the Smalls came less than a week after the principal of Atlantic City High School was indicted in a case stemming from the same incidents.
Constance Days-Chapman was indicted on official misconduct, child endangerment and other charges for allegedly failing to report the alleged abuse of the Smalls' daughter to state child welfare authorities as required by law and school district policy.
Days-Chapman is a close friend of the Smalls; La'Quetta Small is her boss.
According to the indictment, in December the girl, who was 15 at the time, told Days-Chapman she was suffering continuous headaches from being beaten by her parents in their home.
But instead of telling authorities, Days-Chapman instead told the Smalls.
Her lawyer says she is innocent.