If I have an android game based on java native libraries. Is it to possible to compile into a windows/linux executable without a 3rd party emulator?
No, you cannot directly compile an Android project into a non-Android based executable.
You're going to need to port the code out. How easy that will be is going to depend greatly on how you structured your code base. If the game/application logic is separate to that of your Android specific code (think Activities, etc), it should be fairly easy to do, because that's the code that will obviously need to be re-written.
I would take a look at LibGDX to aid this. If you port your game using LibGDX, you'll have both desktop and Android with virtually the same code base.
The short, official answer is no, you can't. Android has it's own specific API's which don't exist for any desktop environment.
That being said, there's things you can do: