Messi, who attended the ceremony at the Chatelet Theatre in the French capital with his wife and children, succeeds Luka Modric, the Real Madrid and Croatia midfielder who won the prize last year.
The Barcelona number 10 previously won the award in 2009, 2010, 2011 and in 2012 before claiming his fifth Ballon d’Or in 2015.
This latest honour comes after he also claimed FIFA’s equivalent award, The Best, in September.
“It is 10 years since I won my first Ballon d’Or here in Paris and I remember coming here with my three brothers, I was 22 and it was all unthinkable for me what I was going through,” Messi said on stage.
“Now ten years on this is my sixth, in a very different time, very special in my personal life with my wife and three children.”
The Argentine added: “I am aware of the age I have but I hope I have several years left to keep enjoying my football and doing this.”
Messi has scored 46 goals in 54 matches so far in 2019, and netted 36 times in total in 34 La Liga matches last season as Barcelona won the Spanish crown.