In this paper, we propose a robust adaptive cubature Kalman filter (CKF) to deal with the problem of an inaccurately known system model and noise statistics. In order to overcome the kinematic model error, we introduce an adaptive factor to adjust the covariance matrix of state prediction, and process the influence introduced by dynamic disturbance error. Aiming at overcoming the abnormality error, we propose the robust estimation theory to adjust the CKF algorithm online. The proposed adaptive CKF can detect the degree of gross error and subsequently process it, so the influence produced by the abnormality error can be solved. The paper also studies a typical application system for the proposed method, which is the ultra-tightly coupled navigation system of a hypersonic vehicle. Highly dynamical scene experimental results show that the proposed method can effectively process errors aroused by the abnormality data and inaccurate model, and has better tracking performance than UKF and CKF tracking methods. Simultaneously, the proposed method is superior to the tracing method based on a single-modulating loop in the tracking performance. Thus, the stable and high-precision tracking for GPS satellite signals are preferably achieved and the applicability of the system is promoted under the circumstance of high dynamics and weak signals. The effectiveness of the proposed method is verified by a highly dynamical scene experiment.