Mr Moon died at a church-owned hospital near his home in Gapyeong, northeast of Seoul, two weeks after being taken to hospital with pneumonia, said Unification Church spokesman Ahn Ho-yeul.
Mr Moon’s wife and children were at his side.
Mr Moon, born in a town that is now in North Korea, founded his religious movement – whose members are often called Moonies – in Seoul in 1954 after surviving the Korean War. He preached new interpretations of lessons from the Bible.
The church gained fame – and notoriety – in the 1970s and 1980s for holding mass weddings of thousands of followers, often from different countries, whom Mr Moon matched up in a bid to build a multicultural religious world. It is estimated he married or blessed millions of couples over the years.
The church was accused of using devious recruitment tactics and duping followers out of money; parents of followers in the United States and elsewhere expressed worries that their children were brainwashed into joining.
The church responded by saying that many other new religious movements faced similar accusations in their early stages.
“International and intercultural marriages are the quickest way to bring about an ideal world of peace,” Mr Moon said in a 2009 autobiography. “People should marry across national and cultural boundaries with people from countries they consider to be their enemies so that the world of peace can come that much more quickly.”
In later years, the church adopted a lower profile and focused on building a business empire that included the Washington Times newspaper, the New Yorker Hotel in Manhattan, Bridgeport University in Connecticut, as well as a hotel and a fledgling car manufacturer in North Korea.
It acquired a ski resort, a professional soccer team and other businesses in South Korea, and a seafood distribution firm that supplies sushi to Japanese restaurants across the US.
The Unification Church claims millions of members worldwide, though church defectors and other critics say the figure is no more than 100,000.
In 2009, Mr Moon married 45,000 people in simultaneous ceremonies worldwide in his first large-scale mass wedding in years.
Some were newlyweds and others reaffirmed past vows.
He married an additional 7,000 couples in South Korea in February 2010. The ceremonies attracted media coverage but little of the controversy that dogged the church in earlier decades.
Born in 1920 in what is today North Korea, Mr Moon said he was 16 when Jesus Christ called him.
While preaching the gospel in North Korea, in the years after the country was divided into the communist-backed North and US-allied South, Mr Moon was imprisoned in the late 1940s for allegedly spying for South Korea – a charge he disputed.