The 32-year-old Argentinian outperformed Cristiano Ronaldo (Torino Juventus) and Virgil van Dijk (Liverpool).
The fair was the 10th time Spain's champion with Barcelona last season and scored 51 goals in 50 games in all series.
The Champions League-winning Liverpool team won the award with Alisson Becker and Jürgen Klopp, respectively, receiving the title of best goalkeeper of the year and best coach of the year.
Megan Rapinoe, who was crowned World Champion for the second time this summer, was outspoken as the best female player of the year, ahead of Lucy Bronze and Alex Morgan.
Gate of the Year (Puskas Prize): Daniel Zsor (Debrecen) vs Ferencvaros (Hungarian High League)
Men's Coach of the Year: Jürgen Klopp (Liverpol)
Men's Player of the Year: Lionel Messi (Barcelona - Argentina)
Men's Goalkeeper of the Year: Alisson Becker (Liverpol - Brasilia)
Women's Trainer of the Year: Jill Ellis (USA)
Women's Player of the Year: Megan Rapinoe (Reign FC - USA)
Women's Goalkeeper of the Year: Sari van Veenendaal (Madridi Atletico - Dutch)
Fan of the Year: Silvia Grecco
Fair Play Prize: Marco Bielsa ja Leeds United
Women's team of the Year: Sari van Veenendaal, Lucy Bronze, Nilla Fischer, Kelley O'Hara, Wendie Rendard, Julie Ertz, Amandine Henry, Rose Lavelle, Marta, Alex Morgan, Megan Rapinoe
Men's team of the Year: Alisson Becker, Virgil van Dijk, Sergio Ramos, Marcelo, Matthijs de Ligt, Frenkie de Jong, Luka Modric, Eden Hazard, Lionel Messi, Cristiano Ronaldo, Kylian Mbappe