A man accused of murdering his girlfriend's seven-year-old son and later blaming it on an accidental fall from a pogo stick has been denied bail.

The man, 29, who cannot be identified, is charged with 28 offences, including murder, common assault, inciting an act of indecency, and assault occasioning actual bodily harm.

The boy's mother, 25, is also charged with murder.

The couple told police the boy died after he fell off a pogo stick at a home in Sydney's south on May 21, 2013.

But it is alleged the couple abused the boy for months before he died.

The man made an application to be released from jail on Monday, arguing the case against him was weak and he needed to be free to prepare for a complex murder trial.

He appeared in the NSW Supreme Court via audiovisual link to hear the decision on Wednesday, wearing prison greens and rosary beads, and waving at relatives sitting in the court.

Justice Lucy McCallum, in denying his application, noted the strength of the Crown case and the risk that he would not comply with bail conditions.

"The charges alleged in brief summary are a series of acts committed by the applicant towards a seven-year-old boy," Justice McCallum said.

"He appears to have earned [his partner's] trust and converted her to a style of parenting which many would find offensive.

"In short ... the murder charge is based in a contention that the applicant forced the boy to stand for a lengthy period of time on a coffee tin." 

Autopsy results cast doubt on the man's version that the injuries were caused by an accidental fall from a pogo stick, Justice McCallum said.

The court heard that an alternative approach to the murder charge would be that he showed "reckless indifference" to the boy's life by not getting immediate help when it was obvious the boy was suffering catastrophic brain damage.

"I do not accept the submission that there's a weak Crown case so far as the charge of murder is concerned," Justice McCallum said.

The man grinned and gestured wildly on screen upon hearing the decision, before the audiovisual link was cut off.

He and the co-accused are due to appear in court later this month.