When linearly polarized light is focused using a high numerical aperture lens with three-zone annular phase pupil filter, vector diffraction method was applied to study the optical intensity distribution in transverse and axial directions. Numerical simulation results show that optical intensity distribution in transverse and axial directions need to be treated simultaneously. When three-zone annular phase pupil filter is added in front of a high numerical aperture lens, transverse super resolution, extended axial focal depth and flat-top focusing can be achieved at the same time. Furthermore, When phase modulation depth is changed, the phenomenon of axial focal shift can be found. The structure of three-zone annular phase pupil filter was optimized and the optimized results were given.