Based on the original unsteady simulation program, the transonic aircraft external store separation was simulated by structured chimera grid approach coupled with a six degree of freedom trajectory code. The chimera grid utilized the hole-map cutting method; the searching efficiency was compared between the stencil walk and inverse map when building interpolation during the procedure. The space format utilized flux difference splitting format FDS based on Roe, moreover adding the min-mod limiter to achieve second order accuracy. The time format utilized the implicit integration and discrete scheme of the Back-Euler method. The three-dimensional trajectory of the store was captured and better fit for the experimental data. The results show that the method is correct and provides a reference for the simulation of the unsteady multi-body separation.