The ninth edition of the annual football review has estimated the Argentina international's value at £161.5million ahead of second-placed Ronaldo on £85.2m and Liverpool's Luis Suarez, whose worth is put at £79.4m.
Chelsea's Eden Hazard and Messi's Barcelona team-mate Neymar complete the top five, valued at £61.2m and £50.6m respectively.
Meanwhile, Ronaldo's Real Madrid team-mate Gareth Bale comes in at seventh, valued at £50.9m, almost £30m less than the world-record £80.6m fee Real Madrid paid Tottenham for the Wales international's services last year.
Colombia striker Radamel Falcao and Argentina winger Erik Lamela have seen their values fall by more than 50 per cent since completing transfers 12 months ago.
Falcao joined Monaco for £48.4m from Atletico Madrid last season and is now worth £22.7m, according to the study, while Lamela, who joined Tottenham for a fee of £28.2m from Roma, is valued at £13.6m.
The 96-page publication also found Real Madrid fielded the most expensive starting line-up ever during their successful 2013/2014 UEFA Champions League campaign with average transfer expenditure per player of over £24m.
By contrast, La Liga winners and Champions League runner-ups Atletico Madrid had average transfer fees of just £3.2m per player.
The CIES Football Observatory uses a database that has been developed since 2005 and will disclose their 2014 World Cup predictions based on their formula within the next week.