The 27-year-old Belgian, who also won the award in 2005, won at Brisbane, Miami, Cincinnati and the season-ending WTA Championships in Doha as well as taking her third title at Flushing Meadows.
Just one year after making a comeback following a break to rest injuries and start a family, Clijsters was voted the top honor in a balloting of players as well as the Player Service award for supporting women's tennis off the court.
"It's really nice to win the Player of the Year award just one year after making a comeback," Clijsters said. "While I didn't think it would come so quickly, I am thrilled.
"This year I met a lot of new girls and it was very nice that so many of them had positive reactions to my daughter Jada as well."
Justine Henin, who returned to the WTA last January, was voted WTA Comeback Player of the Year. She reached the Brisbane final, losing to compatriot Clijsters in her first tournament back, and was the Australian Open runner-up in her first major after a one-year break.
Henin won titles on Stuttgart clay and on grass at 's-Hertogenbosch.
Russian star Maria Sharapova won Humanitarian of the Year for her work as a United Nations Goodwill Ambassador. She visited Chernobyl and spent time with children affected by the disaster there.
Argentina's Gisela Dulko and Italy's Flavia Pennetta won doubles team of the year honors. The year-end world number one duo captured seven titles, including the WTA Championships, and enjoyed a 17-match win streak during the season.
Czech 20-year-old Petra Kvitova, who reached her first Grand Slam semi-final at Wimbledon, was named Newcomer of the Year while Russian Elena Dementieva, who retired from the WTA in October, won the tour sportsmanship award.