He was serving a life sentence after being sentenced by a UN-backed court.
Kaing Guek Eav, known as Comrade Duch, ran the notorious Tuol Sleng prison where thousands of people were tortured and murdered in the late 1970s.
As many as two million people are believed to have died under the Khmer Rouge, a Maoist regime that controlled Cambodia from 1975 to 1979.
Duch was the first senior Khmer Rouge leader convicted of crimes against humanity by a UN-backed tribunal in 2010 and sentenced in 2012.
He passed away on Wednesday, aged 77, a spokesperson for the tribunal said, without giving details of the cause. He had been ill for many years.
"Duch died this morning at 00:52am, on 2 September at Khmer Soviet Friendship Hospital. Details of what he died of, I can't tell," Khmer Rouge tribunal spokesman Neth Pheaktra said.