During the chip manufacturing process, meeting overlay error requirements is essential to semiconductor yield. Measuring equipment of overlay error requires standard samples, which the double-layer grating with precise horizontal alignment can be used as, to verify its capability. Thus, we propose a novel alignment and processing method for layer separated processed double-layer gratings. Firstly, the bottom grating is obtained by holographic lithography . The upper and lower layers are aligned based on the homogeneous period of processing diffraction patten and the bottom grating, and manufactured simultaneously. We conducted an optical simulation of the alignment based on FDTD, setting the bottom grating as Ag material, 50 nm depth, 1μm period, and 50% duty cycle. Principally, the alignment accuracy is comparable with the linear encoder.