In its annual report on the player market, the Swiss-based CIES Football Observatory put Messi's value at 216 million euros ($294 million).
Even though Messi's lower performance levels slashed 19 million euros from his market value, he was still worth almost twice as much as arch-rival Cristiano Ronaldo, second in the ranking on 114 million euros.
CIES said that Messi's higher value was mainly related to his younger age -- he turns 27 this month, while Portuguese icon Ronaldo is already 29.
Ronaldo's heroics this season with Champions League winners Real Madrid meanwhile saw his market value climb by four million euros.
The study also showed that Real Madrid did the worst deal -- in market terms -- for a single player when they spent a record 100 million euros to sign Welshman Gareth Bale from London club Tottenham.
"Real Madrid clearly paid over the odds to convince Tottenham to release the player," CIES said, underlining that Bale's market value was now 37 million euros less than he cost the Spanish club.
Real spent an average of 32.3 million euros per player to build its Champions League squad -- the most expensive line-up on record.
Champions League runners-up Atletico Madrid, who this season also clinched the Spanish title, made do with 4.3 million euros per player.
Other clubs where results outstripped spending included Crystal Palace in England, Elche in Spain, Guingamp in France, Augsburg in Germany and Verona in Italy, the study showed.