An appropriate filter function is the key to successful wavefront retrieval for the wavefront sensor based on pupil phase diversity. The effects of kind and size of filter function on phase retrieval are investigated through several kinds of filter functions and different sizes of filter functions based on the mode of wavefront sensor and Zernike decomposition. Simulation results show that the kind of filter function has almost no effect on retrieval effect as long as the size of filter function is within an appropriate range, such as peak vale (PV) is between π rad and 3π rad for the defocus and PV is less than or equal to π rad for the sphere. The restoring accuracy is gradually decreasing as increasing of filter function size, such as PV is bigger than 3π rad for the defocus and π rad for the sphere. In real application, the kind of filter function can be chosen based on the cost and complex of making filter function while the size of filter function is within an appropriate range.