Ronaldo was announced the winner of the award at the Best FIFA Football Awards which held at Palladium theatre in London on Monday, October 23.
The 32-year-old who won last year's inaugural award helped Real Madrid to a La Liga and Champions League double.
Ronaldo scored 12 goals including a brace in the 4-1 win over Juventus in the final of the Champions League which Real Madrid won for the third time in four years.
Ronaldo's brilliant year is expected to also see him go on to match Messi's record of five Ballons d'Or when France Football Magazine announce their winner in early 2018.
FIFA and France Magazine merged for six years to form the FIFA Ballon d'Or but Ronaldo was the first to win the FIFA Best Player of the Year in 2017 when they split. He also won the Ballon d'Or in 2016.
Messi who scored 54 goals last season as Barcelona won the Copa del Rey finished second behind Ronaldo while his former club teammate Neymar came third.
The voting for the award, equally weighted between national team captains, national team coaches, media and fans, closed last month.