The will face court again on January 23.
The boy was found dead in the early hours of May 21 in a unit at Oatley, in Sydney's south.
Family members had called paramedics, telling them the child had sustained head injuries after falling from a pogo stick the previous day.
But police allege the injuries were not accidental, saying the child suffered a history of abuse.
The man's soliciter Phillip Wilkins told reporters outside court that his client will fight the charges.
Asked if he he maintained the explanation about the pogo stick, he said: "Yes I believe so.''
NSW State Crime Command Homicide Squad Commander Mick Willing on Wednesday described the case as among the most horrific he had ever seen.
The 25-year-old woman is charged with a murder, production of child abuse material, failure of a person with parental responsibility to care for a child, and common assault.
The 29-year-old boyfriend, who was in jail, is also charged with murder.
Earlier this year he was charged with 25 offences including assault, child neglect, taking action resulting in injury or sex abuse and producing child abuse material.
The boy was allegedly reduced to begging for water from shocked campers in the Illawarra two months before he was found dead, the court was told at the man's September bail hearing.
An autopsy showed three fractured ribs, a bruise in the shape of a fist, feet injuries and bruises to the boy's legs, back and buttocks that were inconsistent with normal childhood injury, court papers have previously revealed.
The boy and his two younger siblings had been well cared for but police allege that the situation changed dramatically after the family moved early this year to the man's studio, which was windowless and had no toilet.
- AAP
