Paleokarst reservoirs are the major type of the Ordovician carbonate reservoirs in the Tahe Oilfield. Due to the strong heterogeneity in distribution, it is a real challenge to detect the spatial distribution of paleokarst reservoirs, especially those deeply buried more than 5500 m in the Tahe area. Based on the abundant core samples, this paper first described the structure of paleocaves drilled by well. Second, after time–depth conversions, the results from drilled wells were tied to three-dimensional (3D) seismic datasets, and then the threshold of host rocks and caves in wave impedance were identified. Third, the seismic-scale mapping and visualization of the paleokarst reservoirs were achieved by tracing the distribution of paleocaves. This approach was applied in the well T403 area, and the structure of the paleokarst, especially the runoff zone, was interpreted. 3D structure and spatial distribution of the paleokarst system was demonstrated by plane, vertical, and 3D models. Additionally, according to the hydrology genetic relationships, the paleocaves in the runoff zone were divided into sinkholes, main channel, and branch channel. The approach of a 3D geophysical characterization of a deeply buried paleokarst system can be applicable to Tahe and other similar paleokarst oilfields, which will guide hydrocarbon exploration in paleokarst reservoirs.