Dear Student,
Pitch is a measurement of vibration that you listen fast and rapid vibration means higher pitch.
In an empty bottle you can see that there is lot of space inside the bottle .So it sucks in more air inside flowing in to build up enough pressure to push the air jet again outside and this sucks more inside the bottle that takes long time ,resultantly the vibrates slowly.
But when you fill the bottle with water there is less space inside the bottle which usually takes less time for the pressure to build up . Resultantly vibration happens more quickly and it produces higher pitch .
That is why bottles filled with different water level produces different sound .
Regards