The 36-year-old was recognised at the ceremony in Paris after helping his country win the World Cup in Qatar last year.
Messi won his record-extending Ballon d’Or award ahead of Manchester City forward Erling Haaland.
The Norway international scored a record-breaking 36 goals in 35 league games and hit 52 in all competitions as City won the Treble of Premier League, Champions League and FA Cup.
He was recognised for his achievements with the Gerd Muller Trophy for best goalscorer.
“I want to thank Manchester City, the whole club,” said Haaland.
“I also want to thank my family and all the people around me for making me who I am today.”
Messi moves further out in front of the rest
The Ballon d’Or recognises the best footballer of the year and is voted for by 100 journalists from around the world.
As well as helping Argentina to World Cup glory, Messi also played a key role as Inter Miami won their first trophy – the Leagues Cup – and has scored 11 goals in 14 appearances for the Major League Soccer side.
He has now won three more Ballon d’Or awards than anyone else, with Cristiano Ronaldo having won it five times, most recently in 2017.
The Portugal international, who plays for Al Nassr in Saudi Arabia, was not named on the shortlist for the first time since 2003.