In this paper, we design a novel kind of microwave cavity in TE 01U mode for rubidium atomic clock. The axial and radial magnetic field distributions and the dependence of resonant frequency on size of the microwave cavity of TE 01U microwave cavity were simulated by HFSS, and compared with TE 011 microwave cavity. The results show that the TE 01U microwave cavity has the advantages of high magnetic field uniformity, good direction, high Q-factor and low temperature Sensitivity. The application of TE 01U microwave cavity to vapor cell frequency standard will effectively enhance the signal-to-noise ratio, reduce the influence of temperature sensitivity of physical package, and improve the stability of atomic clock.