The Domain Decomposition Method(DDM) in conjunction with FDFD and Modes Expansion was used to analyze the discontinuity of the rectangular recangular waveguide. In the regular part of the rectangular waveguide, the electromagnetic field was analytically developed by the waveguide modes and in the irregular part the equations of the discrete points were built by FDFD method. The Depres transmission condition was used to connect the adjacent subdomains and the whole domain's solution was achieved by the iterative procedure. Several examples of waveguide discontinuity were calculated. The agreement between the results and that from other methods verifies its accuracy.