An electromagnetism simulation software based on Finite Difference Time Domain(FDTD) theory is applied to simulate the influence of the substrates in a cavity with a rectangular hole. Through changing the number and the size of the substrates as well as the distances between the substrates and the hole in the cavity, time-domain and frequency-domain results can be obtained. Compared to the empty cavity, computation result indicates that the coupling in the cavity will decrease if the number and size of substrates increase and the distance reduces. Compared to the frequency domain curves, it can be found that the substrates in the cavity will change the distribution of resonant points. According to the simulation results, a conclusion is drawn that substrates loaded in the cavity could restrain coupling，and the anti-interference ability of equipment can be improved.