The Ashele ore concentration area is an important area for polymetallic ore concentration in Xinjiang, China. Scholars have made progress in understanding the ore-controlling structures, ore-bearing horizons, and metallogenic age of this area. However, there are still uncertainties about the 3D distributions of plutons, fault structures, and ore-bearing strata, which restrict the development of deep and peripheral ore prospecting and the discovery of new ore bodies in the area. This study proposes a geological–geophysical modeling method based on irregular sections and uses this method to establish a 3D geological–geophysical model based on physical property data, boreholes, surface geological maps, and geophysical data. The model shows that the study area has many hidden rock masses with various depths and shapes and fracture structures with complex shapes. The fault structure in the area is complex, and the ore bodies are controlled by the faults. The ore-bearing geological units (Ashele Formation) exhibit an obvious east–west-trending W-shaped fold structure. The deep part of the northern Ashele Formation extends northward slightly, and the southern Ashele Formation has thick strata, with depths generally greater than 2 km. Based on the information on deep structures provided by the model, three metallogenic prospective areas are predicted, which points out the direction for further prospecting work in the ore concentration area and shows that the adopted modeling method and process have good applicability for constructing 3D models of ore concentration areas with sparse data, large area, and complex geological structures. The proposed modeling method provides technical support for ore prospecting, particularly in the overburden area or ore concentration area with sparse data.