Subsurface river systems constitute one of three major paleokarst types that make up Ordovician reservoirs in the Tahe area of the Tarim Basin. The total length of the river system is approximately 400 km, and the reserves associated with this karst type are more than 200 million tons. However, it is manifested that 47% of drilled wells have not encountered river paleokarst, while 50% of wells that have encountered river paleokarst are fully filled due to the poor understanding of the paleokarst of this region, resulting in a significant variation of production capacities. In this study, we propose a detailed data integration approach with outcrops, drilling, logging, seismic profiles, and dynamic data to delineate the complex paleokarst river system in the Tahe area. The karst geological theory with reservoir characterization is combined in particular. The workflow of clarifying the main controlling factors, architecture types, and development distribution modes of the subsurface river system is established. Fill material type, sequence of fill structure, and fill controlling factors are also revealed. A quantitative characterization method of the subsurface rivers is established adopting predictions based on seismic data and high-resolution geostatistical and geological modeling. The Ordovician reservoirs in the Tahe area comprise three paleokarst river systems with different characteristics. Karst paleogeomorphology is the main control over the overall flow direction and plane distribution of the subsurface rivers. Changes in the surface of the phreatic zone are crucial in controlling the vertical layers and scale of the rivers. The combined action of faults plays a decisive role in controlling the anastomosing pattern of the rivers. Single-branch channels, reticulated channels, and structural corridors in single-layer or multilayer styles are the main subsurface river types. Trunk channels, branch channels, hall caves, and inlets/outlets are dominant structures in the architecture of the river system. Sand-mud, breccia, and chemically precipitated materials are the most common fill types. Three typical sequences of fill structure and four spatial combination modes exist in the subsurface river system. The morphology and fill characteristics of rivers are predictable using seismic attributes, such as frequency division energy, frequency division inversion, and coherent energy gradient. 3D models are constructed by multivariate control multipoint geostatistical method, which can characterize the strong heterogeneity characteristics of subsurface river systems. This complex paleokarst system enables remarkable results for the adjustment of the reservoir development plan through quantitative characterization.