The warrants, unsealed Wednesday, state investigators found a crowbar near mother Christina Anderson's body, and blood next to her head, the Los Angeles Times said.
Hannah's brother, Ethan, 8, was found burned.
The documents do not elaborate on the extent of the torture, but say the abuse occurred before suspect James Lee DiMaggio abducted Hannah, 16.
The warrants also describe the Anderson's relationship with DiMaggio, 40, whom the children called Uncle Jim, the Times said.
Investigators who are determining whether there are co-conspirators have also requested information on two phone numbers DiMaggio called the day of the abduction, the warrants state.
DiMaggio set up a trap on the night of Aug. 4, and asked the family to come to his home so he could say goodbye before moving to Texas.
He then set his house on fire and kidnapped Hannah, with whom he had an "unusual infatuation," police said.
DiMaggio was killed during a rescue attempt Saturday in the Idaho wilderness after a couple spotted him and Hannah earlier in the week. Hannah was taken to a hospital after being rescued.
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