Under the high sea state conditions, considering ocean current disturbance can lead to uncertain covariance statistic of the measurement noise. Therefore, a state estimation method of underwater passive integrated navigation with FCMAP-UKF based on the fuzzy control method is presented. In this method, fuzzy adaptive factor is adopted to improve the adaptive ability and rubustness of the filter by adjusting the uncertain covariance of measurement noise dynamically during the filtering process. Filter results show that the accuracy of the proposed method can achieve the traditional method and in the same time can overcome uncertain noise and disturbance in autonomous navigation system and provide reliable and effective positioning services.