Although deeply coupled Strapdown Inertial Navigation System/Global Positioning System (SINS/GPS) technology has been considered the foremost navigation system in Hypersonic Cruise Vehicles (HCVs) by many research institutions, the wireless signal from the Global Navigation Satellite System (GNSS) is almost completely shielded by the real-gas effect in the hypersonic state, which results in an obvious decline in precision of the deeply coupled INS/GPS. Integrated INS/GNSS/CNS(Celestial Navigation System)navigation systems were adopted for HCVs. However, this increased the complexity of the system and led to the main filters tending to diverge in the information fusion process. Thus, a new method for INS/GNSS/CNS integrated navigation in hypersonic cruising aircraft based on non-Keplerian orbits is presented in this paper. By using the flight characteristics of the HCV, without adding any sensor, the non-Keplerian orbit mode of the HCV is considered to be the fourth virtual sensor; its exact non-Keplerian orbital model and an optimal data fusion model of a SINS/GNSS/CNS integrated navigation system constitute a deeply coupled mode, and the orbital model modifies the integrated navigation system and the integrated navigation system feeds information back to the orbital model. Experimental results indicate that the new method has much better precision with respect to position and velocity than the traditional method; the main filters still achieve effective constringency when they are subject to interference; the precision and reliability of the INS/GNSS/CNS integrated navigation of the hypersonic cruising aircraft are improved. The next step of this paper is to continue the research on the nonlinear filtering algorithm of the integrated heterogeneous navigation sensor.