Based on the geological conditions and characteristics of mineralization present, three-dimensional geological modelling is used in conjunction with previous deep research results, in order to discuss the process of deep mineralization in the Tongling ore district. The structural analysis shows that surface deformation is strong, deep deformation is weak, the surface has mainly experienced brittle deformation, with the possibility of a large number of deep ductile deformations. There is a thrust nappe between the Tongling uplift and the Nanling basin, that is the boundary of the Tongling block, which has resulted in the southwest uplift of the Tongling block. Combined with the deep exploration data, the three-dimensional shape of the main rock masses is interpreted, with three-layer structures in the deep magma chamber. The spatial distribution of magmatic rocks is mainly controlled by the structure. The movement of magmatic hydrothermal fluid is dominated by mesoscale seepage in the deep part and ‘dike’ type upwelling in the shallow part. There is a certain coupling relationship between the ore-forming rock mass and the surrounding rock. The ore-forming age is dominated by the Yanshanian period. Based on the distribution, types and metallogenic characteristics of the deposits, the metallogenic model of ‘layer coupling’ in the Tongling ore district is summarized, with the ‘one body, two belts and a multilayer metallogenic system’ is established, which is significant for the future direction of deep prospecting in the Tongling area.