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 is expected to face the Campbelltown Local Court later today.
During a late night press conference, Acting Superintendent Michael Moroney said said all four people were known to each other and police believed the incident was domestic violence related.
"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 reporters on Monday night.
"Police have located a number of items inside the premises, which would be of interest in regards to the injuries sustained to those people."
He said the 47-year-old man had not previously been charged with domestic violence offences.
The alleged murders follow a four-day police blitz on known domestic violence offenders by NSW Police that resulted in more than 900 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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