The German manager has acknowledged the Barcelona star's skill but believes form should favour his own player.
Liverpool coach Jurgen Klopp has described Lionel Messi as the best player of this generation but stressed Virgil van Dijk should win the 2019 Ballon d'Or.
The Reds defender is a slight favourite for the award to be handed out in December after being named UEFA's best player and also securing top place in this year's Goal 50.
Messi remains firmly in contention for a sixth Ballon d'Or though and did edge out Van Dijk for FIFA's The Best award in September, claiming eight more votes than the Dutchman.
While Klopp is a massive fan of the Argentine, he believes Van Dijk has performed better over the past year and deserves to win the award.
"If you give the Ballon d'Or to the best player of this generation then you should give it always to Lionel Messi. That's how it is," Klopp said.
"But if you give it to the best player of last season, then it was Virgil van Dijk. I don't know exactly how it will work but that is how I see it.
"The best player of all? That's Lionel. Best player of last season? That's Virgil. We will see."
Messi last won the award in 2015 and would surpass Cristiano Ronaldo should he claim a sixth Ballon d'Or.
Luka Modric ended Messi and Ronaldo's strangehold over the award last year but failed to make the shortlist for the prized piece of silverware this year.
Should Van Dijk win, he'd be the first defender since Fabio Cannavaro in 2006 to claim the Ballon d'Or.
Though hopeful his star defender can claim some individual success next month, Klopp's focus remains on Liverpool continuing their strong start to the Premier League season.
The Reds are yet to lose in the league and currently sit eight points clear at the top of the table with their coach hopeful they can remain focused for the next six months.
"If we lost the last game we played under Crystal Palace, then we suddenly would have been just five points ahead and people would talk about different things," Klopp said.
"The main thing is that we stay relaxed about that. We don't think about the points, we don't think about the gap, we think about the next game. Hopefully we can stay that way."
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