A cryogenic cesium atomic fountain clock is a novel clock with the microwave cavity and atomic free flight region placed in liquid nitrogen. On the one hand, the blackbody radiation shift is reduced at cryogenic temperature. On the other hand, the vacuum in the atomic free flight region is optimized, and the background gas collision shift reduced. The microwave resonant cavity is the most important unit in a cryogenic cesium atomic fountain clock. Through theoretical and simulative investigation, this study designs the configuration and dimensions for an optimized microwave cavity. Concurrently, experiments reveal the effects of temperature, pressure, humidity, and other factors on the resonant frequency of the microwave cavity. Combining the theoretical and experimental study, we obtain the resonant frequency difference between the microwave cavity in a cryogenic vacuum and at room temperature and ambient pressure. By subtracting this frequency difference, we adjust the microwave cavity for room temperature and ambient pressure, then vacuumize and immerse it in liquid nitrogen for verification and fine tuning. Finally, we determine that the microwave cavity resonant frequency deviation from the clock transition frequency is 10 kHz with an unloaded quality factor of 25 000, which meets the application requirements of the cryogenic cesium atomic fountain clock.