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Assembly simulation is an important step in the process of digital aircraft manufacturing planning which helps engineers find the defects in the preassembly plan and fix them before practical assembly. In this paper, a simulation system for flexible aircraft assembly is proposed. It uses OGRE and PhysX as the development platform instead of customizing commercial CAD/CAM platforms or implementing the system through OpenGL directly. The reason for choosing open source tools to implement the system is described in detail first. Then the architecture of the system is presented and introduced. Meanwhile, an example is given to illustrate the simulation process which consists of motion simulation and collision analysis. Finally the evaluate system that consists of assembly feasibility analysis, tolerance analysis and ergonomic analysis is described.