The performance of on-board atomic clock directly affects the accuracy of navigation and positioning for users. Evaluating the performance of on-board atomic clock is an important part of the construction and monitoring of satellite navigation systems. With the deployment of the Beidou-3, it is necessary to evaluate the performance of the new generation of on-board rubidium atomic clocks and hydrogen atomic clocks carried by Beidou-3 satellites. In this paper, the performance of the on-board atomic clock is evaluated by three indicators: frequency accuracy, drift rate and stability. From the experimental results, the frequency accuracy of Beidou-3 satellites on-board atomic clock is on the order of E-12~E-11, the drift rate of the rubidium clock is on the order of E-13, and the drift rate of the hydrogen clock is on the order of E-14. The stability of days is on the order of E-14, and the stability of the on-board hydrogen clock is on the order of E-15. Compared with the on-board atomic clock, the hydrogen clock is more prone to large phase jumps, but this jump has little effect on the accuracy index.