The invention relates to the technical field of natural resource investigation and monitoring, in particular to a three-dimensional surface matrix fine modeling method based on multi-source data. Comprising a three-dimensional model modeling method system for establishing an attribute grid model by fusing source data processing, surface dimension raising structural model establishment, voxel model establishment, model entity attribute endowing structured semantic processing and the like, so that ordered and multi-dimensional management and layer control of geoscience data are realized, and the spatial distribution states of different types of surface matrixes are finely represented. According to the technical scheme, the three-dimensional modeling technology for the surface matrix layer between the surface covering layer and the underground resource layer is provided, and visual expression and analysis application of the internal structure relation, space-time evolution and mechanisms for other natural elements of the surface matrix layer are achieved; and the requirements of special investigation and ecological management of typical landform regions can be met.