Are all these usages correct? Is one more natural than another?

Don’t let appearances fool you.

What’s important is

1) not what’s inside but what’s outside.

2) not what’s on the inside but what’s on the outside.

3) not the inside but the outside.

teacherJapanAre all these usages correct?

I think you got the meaning reversed. The outside represents appearances. That aside, they are all unremarkable.

teacherJapanIs one more natural than another?

Aphorisms are not really very natural anyway. I'd say number 2 sounds best, followed by 1 and then 3, but that is a matter of opinion.