Phase grating (PG) mark is a key component of a micro-displacement measurement system. In this paper, a design method of PG mark in resonance domain combining rigorous coupled wave analysis (RCWA) method with differential evolution algorithm is proposed to address issues including insufficient calculation accuracy of scalar diffraction theory and time consuming of parameter traversal design method. Firstly, according to the self-reference interference displacement measurement model, the maximum sum of measured optical signal-to-noise ratio (SNR) is regarded as the evaluation function of grating mark design. The relationship between the number of spatial harmonics and calculation accuracy in RCWA method is studied under different incident light wavelengths, polarization states, and grating periods. In view of the measurement requirement of multi-wavelength illumination micro-displacement, the proposed method is used to design the mark, and it is compared with conventional design methods. The results show that for the PG with period of 3.2 μm, the duty cycle of the grating is 0.484, and the groove depth is 161.5 nm under transverse magnetic (TM) light. Furthermore, the sum of SNR reaches the maximum value of 586.63. Compared with conventional design methods, the proposed method shortens the time in designing the PG mark to 0.2%, and the maximum improvement ratio of the sum of SNR reaches 24.4%.