Halladay pitched a perfect game in May and then threw a no-hitter in the playoffs. In his first season with the Phillies, he led the NL with 21 wins and topped the majors in innings, shutouts and complete games.
Halladay received all 32 first-place votes in results released Tuesday by the Baseball Writers' Association of America.
Adam Wainwright of St. Louis was second and Ubaldo Jimenez of Colorado was third. San Francisco ace Tim Lincecum, who won the past two NL Cy Youngs, finished 11th.
For Halladay, it is his second career Cy Young Award, having won it in the American League in 2003 as a member of the Toronto Blue Jays.
Halladay is the fourth Phillie to win the award, joining Hall of Famer and four-time winner Steve Carlton (1972, 1977, 1980, 1982), John Denny (1983) and Steve Bedrosian (1987).