A detail analysis about the alignment signal of wafer phase grating in the projection lithography processes has been investigated. Based on Fourier optics and matrix optics the model considers that the reflectivity is various over the wafer phase grating with processes layers and resist layer. The alignment structure of resist grating over bare wafer is also described with similar considerations. The calculated results are compared with the experiment data published by others, they are closer to each other. The computer program is also suitable for the analysis of the alignment signal in the lithography with chemical mechanical polish or with antireflective coating.