Jackson is charged with killing 25-year-old Patricia Belizaire of North Brunswick. Her body was found Feb. 22, burning in a park in Ramapo, N.Y.
Jackson also faces a child endangerment charge in New Jersey and a reckless endangerment charge in Delaware.
The couple's 20-month-old daughter was found unharmed but crying in the restroom of a Shell station in Newark, Del., the day before police found her mother's body.
Prosecutors say Belizaire was dead before she was set on fire.
Assistant Prosecutor Nicholas Sewitch of the Middlesex County Prosecutor's Office, which is leading the three-state investigation, said they believe Jackson strangled Belizaire on the morning of Feb. 21 in her North Brunswick home, then drove about 90 miles south to Delaware, where he allegedly abandoned the toddler.
The child was found by a stranger who heard her crying, and she was identified after her photograph was distributed to the news media. The child was alone for less than half an hour before she was found, Sewitch said.
Prosecutors say Jackson then returned to New Jersey and in the early morning hours of Feb. 22, drove to Ramapo, N.Y. where he allegedly dumped Belizaire's body and set it on fire around 5:20 a.m.
George Nassif of New Jersey's Office of the Public Defender entered the plea on Jackson's behalf but declined to comment on the case.
Jackson remains in jail on $2.75 million bail, which includes $2 million on the murder charge and $750,000 on a separate kidnapping charge.