A couple tormented, neglected and abused their children by locking them in cages, tying them up and sexually assaulting them, an Adelaide court has heard.

Jurors were told the young boy and girl faced frequent beatings from their biological father and stepmother, both aged in their early 40s.

The Adelaide District Court heard the children's fingers were slammed in doors and they were tied to trees or locked outdoors as punishment.

The father also raped his daughter, the jury heard.

The man faces six counts of false imprisonment, five of aggravated assault causing harm, two of aggravated indecent assault and two of unlawful sexual intercourse and the woman is charged with two counts of false imprisonment and two of aggravated assault causing harm.

Neither can be named to protect the identity of the children.

The court was told the man allegedly smashed his daughter's head against a wall until she bled.

Another time, the children were gagged and tied together on a kitchen table then photographed while in distress, the court heard.

Items such as a stock whip and a bed slat allegedly were used to beat the children.

When the children were tied to trees, they were sometimes upside down and left for hours, the court was told.

Prosecutor Amelia Cairney told the jury the children were also locked in cages or sheds, including overnight.

"The physical abuse involved acts of violence, including hitting or belting the children, slamming fingers into doors or physically restraining the children by tying them in trees or locking them in sheds or cages for periods of time," she said.

She alleged the children were left outside in the cold or put under cold showers or in cold baths as punishment.

"This ongoing abuse, on the prosecution case, resulted in an environment of fear and degradation," she said.

The court heard the father was sometimes directed by his partner to abuse the children.

The trial before Judge Sophie David and an extended jury of 14 is expected to run for three weeks.