The finite-difference time-domain method (FDTD) is used to simulate propagation of Gaussian pulse in waveguide. According to the dispersive characteristics of waveguide, a new modulate pulse is presented for excitation source of waveguide, and the formulations of pulse width T and modulate frequency are also given. Applications of the technique are presented, and the numerical results are compared with experimental results, and the comparison shows excellent agreement over a wide frequency band.