A fast analysis method, cell modified compact finite-difference time-domain method (CMC-FDTD), is presented to analyze the performance of electromagnetic band gap waveguides. The method calculates band diagrams in orthogonal coordinate system by translating nonorthogonal lattice to orthogonal lattice. It has highly stability for calculating dielectric and metallic material, either TE or TM mode, and reduces the requirement for memory. The comparisons are made among two numerical results and experimental one to validate the method.