To solve the problem of deficiency of rank existing in navigation constellation long-time auto-navigation based on inter-satellite measurement, a method of integrated navigation based on the Inter-Satellite Links (ISL) and X-ray Pulsar was proposed. The fundamentals of this method were described. To rationalize the computational burden, the generalized federated filters were simplified and improved to fuse the measurements based on ISL and X-ray Pulsar. Finally, the simulation was carried out, and the results proved the rationality and feasibility of this method.