The Sun reports Isauro Aguirre allegedly doused Gabriel Fernandez in pepper spray, forced him to eat his own faeces and vomit and stubbed cigarettes out on his skin.
The 37-year-old is also accused of beating the boy with a bat and shooting him with a toy gun.
John Allen, Aguirre's defence lawyer, said his client had admitted murder but denies torturing the young boy.
Prosecutors claim Gabriel was tortured in the eight-months leading up to his death.
The youngster was also reportedly made to sleep tied up in a small cabinet with a sock shoved in his mouth and a bandana over his face.
An autopsy found cat litter and animal hair in the boy's stomach and a shrunk thymus gland 'from being starved.'
The couple had called 911, but the court heard it was not 'to help Gabriel.'
Prosecutor John Hatami said: 'They called 911 to cover up what they did.'
James Cermak, a paramedic for LA County Fire Department, said there was an 'unbelievable' amount of damage to the boy's body when it was found at the couple's apartment.'
Aguirre told investigators that he hit the boy ten times in the head, twenty times in the body and 'admitted that he lost count.'
Fernandez will be tried separately, while four social workers are also being prosecuted because of his death.