The invention provides a spatial complex flexible structure multi-body system dynamics modeling and calculating method. The method comprises the steps of 101, building a three-dimensional model and giving parameters; 102, performing mesh generation on the model; 103, calculating a mesh unit generalized coordinate vector q and a generalized velocity vector; 104, building a mesh model constraint equation; 105, according to the mesh unit type, the generalized coordinate vector, the generalized velocity vector and the constraint equation, building a multi-body system dynamics equation on the basis of a first-class lagrange equation; 106, calculating the built multi-body system dynamics equation, and completing modeling calculating of the spatial complex flexible structure multi-body system dynamics problem. The simple and effective dynamics modeling method is provided for the flexible structure multi-body system, and the calculating efficiency is improved.