The invention discloses an ore concentration area scale area three-dimensional geological modeling method and system. The method comprises a step of obtaining geological survey data which comprises stratigraphic area feature data, tectonic line feature data, occurrence point feature data, drill hole feature data, exploration line feature data, and trenching feature and tunnel feature data, a step of defining the spatial and temporal relationship between stratums, the spatial and temporal relationship between faults, and the spatial and temporal relationship between the stratums and the faults, a step of using a Cokriging algorithm to carry out implicit spatial interpolation on the geological survey data and the spatial and temporal relationships, a step of constructing a virtual geological section according to an interpolation result, a step of editing the virtual geological section, and a step of determining an ore concentration area three-dimensional geological model according to the virtual geological section. The invention provides the ore concentration area scale area three-dimensional geological modeling method and system, and on the basis of ensuring low cost, the accurate modeling of the geology of an ore concentration area scale area can be carried out.