A filtering method, phase-difference filtering, was presented to improve the quality of grating Moiré fringe.Each field of the 4 field scanning reticle was devided into multi-lines with different phases to suppress the high harmonic generations and to improve the signal quality of the Moire fringe. Firstly, the Fourier series expression of Moiré fringe was introduced and various harmonic generations of the Moiré fringe were analyzed. Then, the filtering method to eliminate the second, third and fourth harmonic generations was illustrated with the designed grating patterns. Finally, the validity of the method to inhibit the high harmonic generations was verified through simulations and experiments. Experimental results indicate that the third harmonic generation of the Moiré fringe signal can be reduced by 4.9% and the accuracy can be improved by 0.5 μm with the period of 20 μm. The method is effective, low cost, without increasing the system size and easy to be used in industrial productions.