The analysis and design for the microwave cavity in laser-cooled Rb fountain clock developed by ourselves were presented and the basic parameters of the microwave cavity developed were designed in this paper. Based on the analysis to the factors of affecting the resonant frequency of the microwave cavity, the laws of the resonant frequency with surroundings factors were obtained, which are very important significance to improve the accuracy of the atom clock and to adjust the resonant frequency of the microwave cavity. Finally, the microwave cavity developed was tested and the test results indicated that the performance of microwave cavity met the requirements for laser-cooled Rb fountain clock. The transverse phase shift from the microwave cavity was evaluated by the test results.