Ronaldo was crowned the world's best footballer for a fourth time earlier this month.
"The Ballon d'Or should be Messi's every year as he is the best player in the history of football," said Bartomeu on Tuesday.
"There are other good players but Messi is undoubtedly number one."
Ronaldo was crowned the world's best footballer for a fourth time earlier this month, edging out long-time nemesis Messi, who is a record five-time winner of the award.
The decision was heavily questioned by those at the Camp Nou, especially after Messi's sublime display in Sunday's 4-1 defeat of neighbours Espanyol in the Catalan derby.
But Ronaldo was rewarded for helping Real win the Champions League and leading Portugal to Euro 2016 glory.
The Ballon d'Or has passed back and forth between Ronaldo and Messi for the last nine years, since Brazilian Kaka won the 2007 award.