Real-time and accurate fault detection is essential to enhance the aircraft navigation system’s reliability and safety. The existent detection methods based on analytical model draws back at simultaneously detecting gradual and sudden faults. On account of this reason, we propose an online detection solution based on non-analytical model. In this article, the navigation system fault detection model is established based on belief rule base (BRB), where the system measuring residual and its changing rate are used as the inputs of BRB model and the fault detection function as the output. To overcome the drawbacks of current parameter optimization algorithms for BRB and achieve online update, a parameter recursive estimation algorithm is presented for online BRB detection model based on expectation maximization (EM) algorithm. Furthermore, the proposed method is verified by navigation experiment. Experimental results show that the proposed method is able to effectively realize online parameter evaluation in navigation system fault detection model. The output of the detection model can track the fault state very well, and the faults can be diagnosed in real time and accurately. In addition, the detection ability, especially in the probability of false detection, is superior to offline optimization method, and thus the system reliability has great improvement. Real-time and accurate fault detection is essential to enhance the aircraft navigation system’s reliability and safety. The existent detection methods based on analytical model draws back at at least recently detecting gradual and sudden faults. On account of this reason, we propose an online detection solution based on non-analytical model. In this article, the navigation system fault detection model is established based on belief rule base (BRB), where the system measuring residual and its changing rate are used as the inputs of BRB model and the fault detection function as the output. To overcome the drawbacks of current parameter optimization algorithms for BRB and achieve online update, a parameter recursive estimation algorithm is presented for online BRB detection model based on expectation maximization (EM) algorithm. Furthermore, the proposed method is verified by navigation experiment . Experimental results show that the proposed method is able to effectively realize online param eter evaluation in navigation system fault detection model. The output of the detection model can track the fault state very well, and the faults can be diagnosed in real time and accurately. In addition, the detection ability, especially in the probability of false detection, is superior to offline optimization method, and thus the system reliability has great improvement.