This paper proposes an automatic structure overset grid method, which utilizes the hole-surface optimization with one-step searching, wall-surface grid oversetting, and dynamic overset grid approaches to achieve the high adaptability of overset grids for complex multi-body aircrafts. Specifically, based on the automatic structure overset grids, the method first solves the coupling of Navier-Stokes (N-S) unsteady flow equation and 6DOF motion equation, and establishes the multi-body collision model. Then, the numerical simulation of unsteady flow for complex aircrafts' multi-body separation, the simulation of multi-body separating trajectory and the separation safety analysis are accomplished. Thus, the method can properly handle practical engineering problems including the wing/drop tank separation, aircraft/mount separation, and cluster bomb projection. Experiments show that our numerical results match well with experimental results, which demonstrates the effectiveness of our methods in solving the multi-body separation problem for aircrafts with complex shapes. dynamic overset grids, multi-body separations, CFD PACS number(s): 47.85.Gj, 47.85.MCitation: Zhang H R, Fan J J, Yuan W, et al. Structure overset grid method and its applications to simulation of multi-body separation.