At 23, McIlroy is the youngest Player of the Year honorees since Tiger Woods won in 1998 just before his 23rd birthday.
McIlroy this year won the PGA Championship and, within six days, the Deutsche Bank Championship and BMW Championship in early September. He also won the Honda Classic in March. His 10 Top 10 finishes, tied for most this year, in just 16 tournaments.
He took home the Arnold Palmer Award as the PGA Tour's leading money winner, earning more than $8 million. He claimed the Byron Nelson Award and Vardon Trophy, honors given for low scoring average.
He also took the money title on the European Tour and ends 2012 as the world's top-ranked golfer.
The Jack Nicklaus Award, as the player of the year honor is named, is decided on a vote of PGA Tour members. The PGA didn't provide a vote margin but said McIlroy was selected over Jason Dufner, Brandt Snedeker, Bubba Watson and Woods.
The tour also said John Huh was voted Rookie of the Year. Huh survived a en eight-hole playoff in winning the Mayakoba Golf Classic in February and had four Top 10 finishes in 28 starts.