As expected, the 23-year-old was the popular choice for the annual Jack Nicklaus Award, decided by a vote from eligible tour players, becoming the youngest recipient since Tiger Woods in 1998.
McIlroy won four US PGA Tour titles this year, including the US PGA Championship by a record eight strokes. Nicklaus held the previous record margin for the last major on the golfing calendar, winning the 1980 US PGA Championship by seven shots.
"It's always nice to get recognition from your peers, the guys that you're trying to beat week in, week out," McIlroy said.
"I guess it's just a great way to end what has been a great year and my best season so far."
McIlroy also won the Honda Classic, Deutsche Bank Championship and BMW Championship and the Vardon Trophy for the lowest scoring average.
He also won the money lists for the US PGA and European Tours, making his selection a virtual formality on a final ballot that included Jason Dufner, Brandt Snedeker, Bubba Watson and Woods.
"It's no surprise that Rory McIlroy was voted by the players and his peers as the best Player of the Year," US PGA Tour commissioner Tim Finchem said.
John Huh won the rookie of the year award after becoming the youngest player in more than a decade to qualify for the Tour Championship.
Huh, 22, broke through for his first win at the Mayakoba Golf Classic in February, enduring an eight-hole playoff with Robert Allenby.
The youngest player before him to reach the end-of-season championship was Spain's Sergio Garcia, who was 21 in 2001.