In the APF system, PWM control plays an important role in improvement of power quality and harmonic compensation. Given the current PWM control method assumes DC voltage as constant. So the APF operating loss and energy exchange among system components cause the DC voltage the certain fluctuation which deteriorates the effect of harmonic compensation. This paper presents an improved PWM method which uses the designed fuzzy PID controller to control the deviation between the calculated voltage and the set one, adjust the size of the duty cycle to modify PWM waves, and make the output stability in the new set-point. Finally, it shows the simulation results in this paper. This improved PWM approach makes the AV output to avoid the influence from the DC fluctuation, and obtains the ideal harmonic compensation effect