With the continuous advancement of deep space exploration missions, the solar system boundary exploration mission is established as one of the China's most important deep space scientific exploration missions. The mission of the solar system boundary exploration has many challenges such as ultra-remote detection distance, ultra-long operation time, and ultra-long communication delay. Therefore, the problem of high-precision autonomous navigation needs to be solved urgently. This paper designs an autonomous intelligent navigation method based on X-ray pulsars in the cruise phase, which estimate the motion state of the probe in real time. The proposed navigation method employs the Q-learning Extended Kalman filter (QLEKF) to improve navigation accuracy during long periods of self-determining running. The QLEKF selects automatically the error covariance matrix parameter of the process noise and the measurement noise by the reward mechanism of reinforcement learning. Compared to the traditional EKF and AEKF, the QLEKF improves the estimation accuracy of position and velocity. Finally, the simulation result demonstrates the effectiveness and the superiority of the intelligent navigation algorithm based on QLEKF, which can satisfy the high-precision navigation requirements in the cruise phase of the solar system boundary exploration.