The bodies were found in Sydney's southwest after a call to triple-zero from the home shortly before 8pm on Monday, police said.
Officers entered the home on Raymond Avenue in Campbelltown and found the bodies of two boys, aged four and 12, and a 46-year-old woman inside.
A 47-year-old man was arrested at the scene and taken to Campbelltown Police Station, where he was charged with three counts of murder and refused bail.
He will face the Campbelltown Local Court later today.
Acting Superintendent Michael Moroney said police believe the three victims were the arrested man's wife and children.
Despite the horrific nature of the crime, police had no prior knowledge of domestic violence incidents at the home.
"Whilst I can't give you specific information in regards to how they passed, what I can tell you is that all three persons sustained significant injuries and it was a particularly violent crime scene," Supt Moroney told ABC News on Tuesday.
"What this does is really highlight the scourge that domestic violence is across society."
The alleged murders follow a four-day police blitz on known domestic violence offenders by NSW Police that resulted in nearly 1000 arrests.
Between Wednesday and Saturday, 993 people were arrested and 2063 charges were laid, with 299 arrest warrants executed.
Police also seized 94 guns and 48 other weapons during Operation Amarok.
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