The Barcelona star beats Liverpool's Virgil van Dijk and Juventus' Cristiano Ronaldo to scoop the prize.
Messi was on course for a historic season but Barcelona suffered defeats in the Champions League semi-final and the Copa del Rey final.
But those disappointments didn’t take away from what was a brilliant individual season for the Argentinian.
He netted 51 goals in 49 appearances in all competitions - it certainly wasn’t his fault that the Blaugrana blew a 3-0 advantage against Liverpool.
His competitors for the award Ronaldo and Virgil van Dijk also had a good season.
The Portuguese scored 21 goals as Juventus won the Serie A, while Portugal emerged champions of the UEFA Nations League.
Van Dijk was a pillar at the Liverpool defence as helped protected their goal area in their UEFA Champions League triumph. The Reds also lost the Premier League to Man City by a point, the Dutch defender in the thick of event.
He also produced a standout performance as the Netherlands finished runners-up in the UEFA Nations League.