Kroos was fiercely critical of the decision to name Messi as the winner before also revealing who he voted for in his top three.
Lionel Messi has been criticized after winning the 2021 Ballon d'Or.
Real Madrid midfielder Toni Kroos and club legend Iker Casillas both said the decision to is 'absolutely not deserved'.
Messi who plays for Paris Saint-Germain saw off competition from Bayern Munich striker Robert Lewandowski and Chelsea midfielder Jorginho to lift the seventh Ballon d'Or of his incredible career.
Reacting, Kroos was very critical of the decision to name Messi as the winner before also revealing who he voted for in his top three.
Speaking on his podcast, Kroos said: 'It's absolutely not deserved.
'There is no doubt that Messi, with Cristiano, has been the player of the last decade, but this year there should've been others ahead of him.'
Kroos said his top three were Real Madrid team-mate Karim Benzema, Lewandowski and Jorginho.
Iker Casillas, the legendary former Real Madrid goalkeeper who had some sensational battles with Messi during his career, also admitted the PSG star should not have won the prize.
The Spaniard added: 'It is increasingly difficult for me to believe in football awards.
'Messi is one of the best but you have to know who is the most outstanding player after the season. It's not that hard.'
After winning the award, Messi did acknowledge Lewandowski's achievements over the past two years and said he did 'deserve' the prize.
Messi said: 'You deserve your Ballon d'Or. Last year everyone agreed that you were the winner.
'I think France Football should give you your Ballon d'Or. You have to have it in your house.'
See how football fans reacted below:
@KevCawood wrote: 'I think him winning it this time shows how ridiculous the award has become. Lewandowski and Salah have been head and shoulders above Messi this year.
@redikki agreed, posting: 'Wonderful footballer, possibly the greatest ever but time @francefootball to shake up the voting. How can #Lewandowski score so many goals over the last 24 months and not get recognised! Giving up on this award!'
@CalumClark13 commented: 'Joke of decision, I know your a barca man but this year and it being suspended last year stinks of corruption both Lewandowski and Salah were better players this year but this has happened before with Messi and Ronaldo where there whole hype and name drop takes over.'