The $20.4 million (£15.4 million) guaranteed annually that Messi receives from Inter Miami remains far ahead of other players.
The figure does not include other types of income, such as his extensive portfolio of sponsorships, which the Argentinian star received as part of the contract he signed upon his arrival in Miami in mid-2023, which concludes in December.
The Argentina captain will begin a three-season extension with Inter next year, the financial details of which are not yet known.
Messi, 38, has just been crowned top scorer of the regular season - with 29 goals in 28 matches - and is favoured to retain the Most Valuable Player award.
His salary tops the list published by the MLS Players Association.
South Korea's Son, the star signing of the US summer, ranks second with the $11.1 million (£8.4 million) annually established in his contract with LAFC.
The former Tottenham captain landed in California in August after the most expensive transfer in MLS history, estimated at $26 million.
His impact has been immediate, with Son producing nine goals in 10 matches as LAFC advanced to the MLS Cup playoffs.
The third spot on the list is occupied by Spaniard Sergio Busquets ($8.7 million), who will retire at the end of the season with Inter Miami.
Paraguayan Miguel Almiron ($7.8 million ,£5.9 million) is in fourth place, and Mexican Hirving "Chucky" Lozano ($7.6 million, £5.7 million) is in fifth, both notable signings for this season by Atlanta United and San Diego FC.