The Barcelona superstar endured a miserable 2020 as his side went trophy-less last season.
However, Kroos reckons he doesn't deserve to be in the top three based on his year for Barcelona.
Speaking on his podcast that he shares with his brother, the German supported Lewandowski while taking exception with Messi's inclusion.
"Lewandowski deserves it, absolutely," he said via AS.
"But for me, Messi does not belong in the top three. I don't think he did well this year."
The Real Madrid midfielder also had his say on the men's coach of the year which Jurgen Klopp won ahead of Bayern Munich boss Hansi Flick.
The Liverpool manager beat his fellow German and Leeds United's Marcelo Bielsa to The Best prize.
On Klopp pipping Flick to the award, he said: "Of course they are both great coaches, based on their successes, Klopp has also had an amazing year.
"You can see it in both of their seasons. In the end, it's not that important either."
On Flick, he added: "Hansi Flick is one of the characters of 2020.
"He not only made his team a triple winner, but he has swept every team and they have rarely scored less than four goals."
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