In this paper, an accurate and efficient full wave analysis for millimeter wave quasi-periodical structure for antenna applications is realized. By extracting all the surface wave poles of the spectral domain multilayered Green's functions, the discrete complex image method (DCIM) can be adopted to fast evaluate their counter parts in spatial domain, and the mixed potential integral equation (MPIE) for method of moments (MoM) can be constructed. With the Jerusalem cross as a patch element on a dielectric layer, a quasi-periodical structure can be organized as the geometries gradually varied. By illuminate this kind of structure with an incident plane wave, the distribution of electric current on the metal surface can be obtained by solving the MoM equation and the forward scattering cross section can be fast calculated by the conjugate gradient (CG) algorithm written in CUDA and realized in NVIDIA graphic process unit (GPU). A layered structure with a 17×17 Jerusalem crosses at 30GHz was calculated and very good agreements have been found between the proposed method and commercial EM simulator (CST), while an improvement on efficiency is realized.Index Terms -Quasi-periodical structure, layered structure, MoM, multilayered Green's functions, CUDA.