Abstract: In order to suppress the Doppler effects in pulsar signals caused by spacecraft velocity, a novel method of X-ray pulsar navigation based on direct/indirect hybrid velocimetry was proposed. The direct velocimetry method provided velocity information directly according to the distorted pulsar profile. It had high accuracy, but was only suitable for high flux pulsar, namely Crab pulsar. A distorted profile matching estimation method for direct velocity and distance measurement was proposed. The indirect velocimetry method was to establish the relationship model between velocity and pulsar time-of-arrival, and provide velocity information by Kalman filter indirectly. The signal-to-noise ratio of low flux pulsar distortion profile was very low, which could not reflect the weak pulsar distortion. Therefore, the indirect velocimetry method was suitable for low flux pulsars. Based on this, the direct velocimetry method and the indirect one were used to update the Kalman filter in turn. And the Kalman filter was used to provide high-accuracy navigation information. Simulation results show that the accuracy of X-ray pulsar navigation method based on direct/indirect hybrid velocimetry is 15% higher than that of the indirect pulsar navigation.