France Football reports that Beckham will earn €36 million in 2012-13, leaving him just ahead of four-time Ballon d'Or winner Messi.
Beckham, who left the Los Angeles Galaxy in December, is reported to have earned an annual salary of €1.7 million, with his income supplemented by €1.3 million in bonuses and some €33 million from other sources, including advertising deals.
The 37-year-old Beckham revealed after signing for PSG that all money due to him from his contract with the French giants would be donated to charity.
In contrast, Messi's income of €35 million includes 13 million in salary and bonuses, with the remainder coming from advertising and other sources.
Ronaldo comes in third, with total income reaching €30 million, including €13.5 million from salary and bonuses.
The magazine also reports that Real Madrid coach Jose Mourinho is the best-paid coach in the world game, earning €14 million a year.
Behind him are two Italians, Carlo Ancelotti at Paris Saint-Germain (€12 million), and Marcello Lippi at Chinese club Guangzhou Evergrande (€11).