The design of excitation sources was presented and the characteristic of waveguide was analyzed with multi-domain pseudospectral time-domain (MPSTD). The cut-off frequency of 2D waveguide and the S parameters of typical 3D waveguide model were calculated with the MPSTD. All numerical results were compared with the HFSS or the FDTD results, which display that the MPSTD is more accurate and efficient. This paper offers a scheme for analyzing the complex waveguide accurately, and extends the application field of MPSTD.