Pulsar navigation is a promising autonomous navigation system for spacecraft, which is applicable to the entire solar system. However, the pulsar’s directional error and the onboard clock error are two types of systematic errors that seriously reduce navigation accuracy. To solve this problem, a star angle/double-differenced pulse time of arrival(SA/DDTOA) integrated navigation method is proposed. Since measurements obtained by observing different pulsars contain the same clock errors, the measurements can be differed to eliminate the common clock error. Then, the pulsar-differenced measurements at neighbor filtering time can be differed to suppress the effect of the pulsar’s directional error on navigation precision. Star angle is used to obtain absolute navigation information, which denotes the angles between the light of sight of Jupiter and that of its background stars. Simulation results demonstrate that the proposed method can eliminate the influence of the onboard clock error and greatly weaken the effects of the pulsar’s directional error. The navigation accuracy is better than the traditional star angle/pulse time of arrival integrated navigation method and star angle/pulse time difference of arrival integrated navigation method. In addition, the navigation accuracy of the SA/DDTOA integrated navigation method is less affected by Jupiter’s ephemeris error. This work greatly reduces the influence of common systematic errors in pulsar navigation on navigation accuracy.