To improve the position accuracy, a CNS (Celestial navigation system)/pulsar integrated navigation system with clock drift is proposed. In the pulsar navi- gation subsystem, the epoch-di®erence method is adopted to eliminate clock drift, but it induces colored noise. The two-level ¯lter, which is composed of an UKF (Unscented Kalman ¯lter) and an H1 ¯lter in series connected, is proposed for fusing the data from the celestial navigation and pulsar navigation subsystems. The celestial naviga- tion subsystem adopts the UKF because of its good perfor- mance in nonlinear estimation, while the pulsar navigation subsystem utilizes the H1 ¯lter due to its robustness to colored noise. Compared with CNS and two CNS/pulsar integrated navigation methods without two-level ¯lter, the proposed method can provide higher navigation accuracy. Simulation results show that the position estimation ac- curacy of the proposed method can achieve 140m in the presence of clock drift.