San Bernardino County sheriff's deputies responded to the home in the 6700 block of Merito Avenue after someone reported a man screaming for help inside the home.
A man, 35-year-old Ian Anthony Roderiquez, was found inside and was arrested. Neighbors identified Rodriguez as the father.
The boy, identified as Richard Roderiquez, was declared dead at the scene.
Two boys and two girls, ranging in age from 8 to 13, were taken to a local hospital in unknown condition, but were expected to survive. Two of the children were set to be released to Child Protection Services and two other children remained at the hospital.
The mother of the children, 35-year-old Sujal Roderiquez, was critically injured and was undergoing surgery, investigators said.
Neighbors said they heard screams in the morning, but were not too concerned since yelling was often heard coming from the troubled home.
They said the mother and four of her children came out covered in blood.
"They just took her right away and slowly they were bringing the kids out and they had blood on them, too, their faces were swollen," said neighbor Sofia Symeou.
Investigators said Rodriguez is being charged with one count of homicide, five counts of attempted murder and six counts of torture.
The Associated Press contributed to this report.