To improve the precision and robustness of Unmanned Aerial Vehicle (UAV) integrated navigation systems, this paper presents an Interacting Multiple Model (IMM) navigation algorithm based on a Robust Cubature Kalman Filter (RCKF) with modified Zero Velocity Update (ZUPT) method assistance. This algorithm has a two-level fusion structure. At the bottom level, the Global Positioning System/Inertial Navigation System (GPS/INS) integrated navigation model and the Dynamic Zero Velocity Update/Inertial Navigation System (DZUPT/INS) integrated navigation model are established by modifying the Zero Velocity Update (ZUPT) method. Subsequently, the RCKF algorithm adopts a robust factor to weaken the influence of measurement outliers on the filter solution. At the top level, the estimation results of the GPS/INS integrated navigation model and the DZUPT/INS integrated navigation model are fused by the IMM algorithm. In addition to enhancing the robustness of filter estimation in the presence of measurement outliers, the proposed navigation algorithm also corrects navigation errors with ZUPT method assistance. Simulation and experimental analyses demonstrate the performance of the proposed navigation algorithm for UAVs.