The nonlinearity between projector output and CCD input deformed fringe intensity in phase measurement system results in spectrum aliasing and affects measurement accuracy. In order to eliminate the nonlinearity relationgship between them and improve phase measurement accuracy, the basic causes of system nonlinearity are analyzed, and a new phase measurement method based on system nonlinearity correction and filtering is proposed. Firstly, the system nonlinearity caused by the gamma distortion in the projector is corrected. Then, the output spectrum is filtered by low-pass filter, only the fundamental frequency component of the spectrum is retained. Finally, the phase measurement of deformed fringes is carried out by four-step phase-shift method. The results of MATLAB simulation and practical experiment show that the proposed method has better effect of system nonlinearity correction and filtering, and is helpful to improve the phase measurement accuracy.