The resonant frequencies of the waveguide microcavity in the two-dimensional rectangular lattice photonic crystal are computed by using the Finite-Difference Time-Domain（FDTD） and Fast Fourier Transform（FFT） methods and the effects of the variations of the radius of dot defect dielectric rod and the refractive index of the background material on the resonant frequencies investigated.The results show that the resonant normalized frequency decreases with the increase of the radius or the refractive index.When the radius increases to 0.45r

normalized frequency of the resonant center is 0.336 and the transmission coefficient of the waveguide microcavity reaches a maximum of 98.02%.