What does this mean in English Que no sea lo que estoy pensando?

"Que no sea lo que estoy pensando" would be something like "That is not what I might be thinking".

It is not the best syntax. Probably something like "Eso no es lo que estoy pensando" would be clearer.

If you use "sea", it puts this into the subjunctive mood, and expresses doubt or uncertainty. "Eso no sea lo que estoy pensando" would be something like "That might not be what I'm thinking."