I have a simple cube which is scale and rotated. When I try to apply rotation and scale. Its get applied but why the cube rotate from its angle. It was rotated in 63 degree. After applying the rotation and scale it in the vertical direction.
Actually your object is not a cube mesh, the box we see is the bounds you can display around your object in the viewport:
As you've rotated your object, it has been rotated as well:
If you apply the rotation, it doesn't rotate the object, that's what we are expecting, but it resets the bounds box, which is also expected for an object that has now a rotation of 000: