Abstract: The Anhui Laboratory of Advanced Photon Science and Technology has beer developing a 6 MeV compact microtron, which can be used to drive compact microfocus X-ray sources or compact terahertz free electron lasers. To achieve a more compact accelerator design, the CST Electromagnetic suite was used to design and calculate the second type RF cavity of the microtron. The frequency of the RF cavity is 2998.2 MHz, and an accelerating voltage of over 1 MV can be obtained in the RF cavity gap. The electron energy gain can reach about 0.9 MeV per pass. At the same time, CST Particle Studio was used to simulate the electron generation and acceleration process in the ultra-high frequency cavity with thermionic cathode. The effects of microwave power amplitude, magnetic field strength, cathode emission position, and beam channel on the microtron were studied. The coupler design considering beam loading was also completed, and the operating parameters of the RF cavity during steady-state operation were obtained. The simulation results show that when the beam loading reaches steady state, with a cathode emission capacity of 20 A/cm², a current of 24 mA can be induced, a beam energy of 6 MeV, an energy spread of 0.64%, and a transverse RMS size of 3.3 mm × 1.8 mm can be obtained.