In highly dynamic and rapidly changing battlefield environments, satellite navigation systems are often in a denied state. The navigation system accuracy of heterogeneous missile flight formations, originating from different sources and equipped with different navigation sensors, is severely affected, resulting in limited flight range. To address this challenge, a novel cooperative navigation system for heterogeneous missile clusters has been designed. This system relies solely on inter-missile data link ranging information and employs rank-deficient constrained cascaded filtering technology to achieve real-time correction of navigation errors within the nodes of the heterogeneous missile cluster. Digital simulation verification and UAV flight test results indicate that the proposed method can effectively improve the navigation accuracy and adaptability of heterogeneous clustered missiles in complex battlefield environments, providing significant reference value for the design of navigation systems in future formations of networked weapons.