Edgar Ray Killen, 92, was jailed 2005, over four decades after he plotted the killings.
Killen died on Thursday night was pronounced dead at the hospital at Mississippi State Penitentiary, correction officials said.
The cause of the “Mississippi Burning” murderer's death would be known after an autopsy but was not thought to be suspicious.
His conviction came on the 41 years to the day since the crime took place and resulted in Killen receiving a 60-year prison sentence—the maximum jail time of 20 years per each victim.
James Chaney, Andrew Goodman and Michael Schwerner were slain by the KKK, local law enforcement officers and others in Philadelphia, Mississippi, on June 21, 1964.
Chaney, a 21-year-old black man and Schwerner, 24, and Goodman, 20, both white New Yorkers, were part of a campaign to register black voters in the South during the “Freedom Summer” becoming known to Klansmen when they came to Philadelphia.
The 2005 trial revealed how the three men were taken into custody on a speeding charge, with law enforcement tipping off the KKK about their whereabouts.
Killen assembled a mob that chased and killed them upon their release, burying the bodies near his property in a 4.5-metre-deep grave.
After their disappearance made national news, federal agents were sent to the area to search for them.
But their burial site was only discovered 44 days after the killings thanks to an informant.
Their deaths sent prompted a public outcry, which some historians say helped turn favour civil rights legislation.
The incident also inspired 1988 Oscar-winning film Mississippi Burning, which is a fictionalised take on the events.