VIENNA three level rectifier is widely used in wind turbine systems, UPS systems,etc. To improve its power quality, the mathmatical model and multi-loop control structure are built under d-q synchronous coordinate system, based on the important requirment for grid side currents and rectifier side voltage in unit power factor operation condition, the reason for currents distortion at zero-crossing point by using multi-loop control and conventional carrier-based PWM method under d-q rotating coordinate system is deeply studied To reduce the total harmonic distortion rate of grid side currents, the way to add compensation component to three-phase reference modulation voltage to eliminate the area that disobey the important limiting condition is applied, the currents distortion around zero-crossing point is inhibitted and the power quality is improved. The rectifier model is built in Saber simulation system, the correctness of theory analysis is proved by comparing the value of currents total harmonic distortion before and after compensation component is added in carrier-based PWM method.