This paper presents an alignment method to improve the projection lithography accuracy for linear scale, which is one main component and measurement benchmark of grating linear displacement sensor. The adjacent pixel gray square variance method of CCD image is used to find the best position of the focal length of the motherboard and then realize the alignment on focal plane. Two image positions in the focal plane from the CCD are compared the traits overlap through the image splicing principle, and to establish the correction of four typical errors basis on the whole grating errors. At the same time, using the rotation error of the mask to summarize Grayscale Variation Function of CCD Image, and threshold functions are used to express the factors including wave crests of the amplitude, period error and phase error, which govern the rotation accuracy and weight alignment accuracy expression of the four error factors is established. In the experiment, it is finally corrected the slope of the mask and be adjusted the same direction of the slide plate with the help of dual-frequency laser interferometer, the influence of alignment error on lithography accuracy was discussed and verified in the static case and the CCD maximum resolution pixel corresponds to 0.1μm, the accuracy of scale is 0.79μm in only 200mm measurement range.