Church officials said Moon, 92, who had suffered complications from pneumonia, was taken to hospital in Seoul in mid-August and was moved to a hospital in a rural retreat last week when his family believed there was little chance of recovery.
His body was lying in a vast building resembling the White House at the retreat in rugged hills about an hour outside the South Korean capital of Seoul. The funeral will be on September 15, after which he will be buried at the retreat.
Moon had led an active public life until recently, officiating a mass wedding for 2,500 in March and leading a service of more than 15,000 followers in July.
Critics have for years vilified the church as a heretical and dangerous cult and questioned its murky finances and how it indoctrinates followers, described in derogatory terms as “Moonies.”
Moon is survived by his wife – the pair are called “true parents” by followers – and 10 of their 13 children.
Religious experts say Moon will remain at the centre of the church, keeping it together despite signs of previously unimaginable fissure among his sons, according to a creed that had been prepared since a helicopter crash four years ago that nearly killed Moon and his wife.
Born in what is now North Korea in 1920, Moon founded the church soon after the Korean War that ended in 1953, rapidly expanding the ministry internationally and building a business at the same time that served as the backbone of the empire.
The Unification Church runs the Segye Times newspaper in South Korea and more than a dozen other firms along with overseas businesses, including the conservative Washington Times.
“The Unification Church will continue to be in good shape even after Sun Myung Moon’s death,” said Tark Ji-il, who teaches church history at the Busan Presbyterian University.
“The Unification Church is not simply a religious organisation, but is a commercial organisation built on religious conviction.”