In order to extend the depth of field and enhance the resolution of microscopy system, a phase pupil filter with Zernike polynomials is proposed. Through analysis of intensity distribution near the focus point, its improvement for optical imaging system is demonstrated. Results show that depth of field is extended 4.15 times as well as resolution is increased 1.3 times. In addition, the performance of Zernike phase pupil is compared with the other phase pupil filters manifesting its advantages. This new type phase pupil with Zernike polynomials has practicability and applied value in flaw detection with microscopy.