Abstract: The finite-difference time-domain(FDTD) method is widely used to solve electromagnetic problems in computer simulation. Some common problems for design of excitation source in waveguide are discussed in the first instance. According to the propagation property of electromagnetic wave, a new method is presented for simulating the excitation source in waveguide simply. The formulas of this method and the special processes are also presented. Results show that FDTD method can simulate complex situation and eliminite the false reflection on the boundary of the excitation source. Comparing with comventional methods, the validity and advantage of this method are proved by computing magnetically insulated transmission line oscillator(MILO) as an example.