Building 3D geological model and numerically modeling its geodynamical processes have become an effective method to research the geological processes. In this paper, it is suggested that the hexahedral model is built in GOCAD by analyzing characteristics of GOCAD and FLAC3D data file, and complex geo-system modeling in FLAC3D is finished through the date interface program. The 3D dynamical model of Dongguashan deposit has been established with this method. The result shows that the modeling process is simple and practical and the model has well computability. So this method for 3D geodynamical modeling is worth popularizing.