A three-dimensional entity unit modeling method of a gear system comprises the steps that firstly, according to the structural characteristics of the gear transmission system, HYPERMESH software is used for preprocessing a complex structure, three-dimensional entity unit models of a gear substructure and a transmission shaft substructure are established respectively, and accurate division and optimization of grids are carried out; then, ANSYS software is used for carrying out modal analysis and extracting a mass matrix and a rigidity matrix; then, nonlinear factors such as time-varying rigidity are considered, and gear tooth meshing of the gear transmission system is modeled through the Pasternak elastic foundation beam theory; finally, according to the interface displacement coordinationcondition, integrating, coupling and dimensionality reduction are conducted on the models of the transmission shaft, the gear and the bearing system through a modal synthesis method, and a high-precision gear transmission system dynamic model matched with the dynamic characteristics of the equipment is established. According to the method, the model precision can be guaranteed, and the calculationefficiency can be remarkably improved, so that a more efficient and accurate method is provided for quantitative analysis of the vibration of the gear transmission system.