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X-ray pulsar-based navigation (XPNAV) is one of the perfect ways for autonomous deep-space navigation in the future. Due to spacecraft state model errors and strong cosmic background noises, low navigation accuracy is one of the main problems in XPNAV. This paper proposes a robust navigation filtering method to reduce the serious effect of spacecraft state model errors and strong noises on XPNAV. This method uses state model errors and pulsar observation errors to estimate and correct the state model. And then, to predict the spacecraft’ state in the next moment with high precision, the gain matrix is adjusted in quasi real-time by using the fading factor to ensure a minimized state estimation error variance in the next moment and an orthogonal residual sequence at different times. Finally, experimental results of multi-group simulations show that the proposed method had significantly improved navigation accuracy. And the accuracy of the proposed method is better than that of $\text{H}\infty $ robust filter and STUKF, especially when the state model errors and noise are great. Under the same conditions, compared with the other two methods, the proposed method has the minimum navigation filtering error and the strongest robustness.