Messi tormented Manchester City last night as Barcelona won 1-0 and 3-1 on aggregate to progress to the quarter-finals of the Champions League.
The Argentine's future at the Nou Camp has been under scrutiny in recent months following reports he had a bust-up with coach Luis Enrique.
But Henry insists it is only natural for Messi to have an ego.
"I'm sad for him, and upset because people doubt him sometimes," Henry told Sky Sports.
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Lionel Messi in action for Barcelona against Manchester City last night
"They doubt him. How can you doubt a guy like that?
"He put himself on a level where it's impossible for me to hear people doubting this man. What he has done we should all enjoy the guy, like we did tonight. It is a pleasure.
"He has an ego. Of course he has an ego. Do you think you do that without having an ego? It's not a bad thing. Having an ego is not a bad thing. Knowing that you are good. You need that.
"Let's all be honest. You need that. He just plays. If you ask him to play with you now just outside the dressing room, he will just want to have fun, perform and be the best out there."
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