The Argentine icon helped guide the club to the top of the Eastern Conference standings and their first ever Supporters' Shield title.
Messi was the joint-second highest scorer in the regular season on 20 goals alongside Denis Bouanga of Los Angeles FC and teammate Luis Suarez.
He also assisted 16 goals across his 19 league appearances, although missed nearly half of their matches throughout the campaign.
The 37-year-old was out for Inter Miami for 62 days having played at the Copa America with Argentina and been injured in the final.
However, Messi clearly still, made enough of an impression to become the latest recipient of MLS' prestigious individual accolade.
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The Landon Donovan MVP award, name in honour of the Los Angeles Galaxy record scorer in 2015, is voted by players, the media and clubs.
As revealed by MLS on Friday, Messi has won the prize for the 2024 season by gaining a majority 38.43 per cent of the vote.
Cucho Hernandez of Columbus Crew came second on 33.70 per cent and Portland Timbers' Evander is third with 9.24 per cent.
Ex-Premier League striker Christian Benteke won 7.10 per cent of the vote with D.C. United and Inter Miami's Suarez is fifth on 2.71 per cent.
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Messi follows Christian Gomez, Guillermo Barros Schelotto, Diego Valeri and Luciano Costa as the latest Argentine MVP award winner.
He is also the first recipient in Inter Miami colours since they entered the MLS in the 2020 season.
"Truly, it is an honour for me to receive this award from all of you," he said to academy players during a surprise ceremony at their Chase Stadium. "It's a source of pride to watch you all train.
"I'm very happy to be here every day. I'm very happy to be in this city, in this club that is growing… It's a pleasure to see you grow day by day. I invite you to keep fighting and striving for your dreams."
Inter Miami finished top of the Eastern Conference on 74 points, eight ahead of Columbus Crew, after winning 22 of their 34 matches.
They lifted the Supporters' Shield by having the best overall record during the MLS regular season.
However, they couldn't make it past the first round of the MLS play-offs as they lost to Atlanta United over three matches,
Inter Miami were therefore unable to go all the way and win the MLS Cup, which is played tomorrow between LA Galaxy and New York Red Bulls.