Abstract: In order to calculate the storing process and dumping process of energy in high quality factor resonant cavity, the input iris and the output coupling structure are modeled as a 2-port net and a 3-port net respectively, and an algorithm based on iteration is proposed according to the signal flow graph of the high quality factor resonant cavity. The algorithm is then used to design a high quality factor resonant cavity working around 2.92 GHz and based on rectangular waveguide of type BJ32. When the width of the input iris takes 20 mm and the width of the output iris takes 60 mm, the resonant frequency, the storing time, the pulse width of the output pulse, the peak output power gain and the energy efficiency are calculated to be 2.9198 GHz, 2.6 μs, 6.82 ns, 129.6 and 0.169, respectively.