Formal/Literal:
* Tout n'est pas ce qu'il paraît. (This is the most direct translation and is quite formal.)
Informal/More idiomatic:
* Les apparences sont trompeuses. (This is a common idiom that literally means "appearances are deceiving.")
* Ce n'est pas ce que ça a l'air. (This means "it's not what it looks like.")
* Il y a plus qu'on ne voit. (This means "there's more than meets the eye.")
More specific:
* Il ne faut pas se fier aux apparences. (This means "don't judge by appearances.")
* La réalité est bien différente. (This means "the reality is very different.")
The best way to choose the right phrase depends on the context and the tone you want to set.