With the simplified dynamic condensation method presented in this paper the dynamic effects of a substructure’s internal DOF can be taken into account in dynamic analysis of a multi-substructure system. Better accuracy is obtained both in the eigen-pairs from free vibration analysis and in the higher-mode responses from dynamic response analysis compared with the static condensation method. In some cases, neglect of the effects of internal DOF or the higher modes may result in substantial errors. Using the method presented in this paper, such errors can be greatly reduced. Moreover, the simplified method is nearly as simple in form as the static method, and thus it is not difficult to implement in multi-substructure systems.