Accurate delineations of the formation chronology and sedimentary characteristics of underground rivers are crucial for prospecting karst reservoirs. Based on drilling records, core samples, seismic data, and thin-section microscopy, qualitative and quantitative analyses of the fillings within the S65 karst channel, located within the erosional zone of the Tahe Oilfield Conventional seismic data, acoustic impedance inversion seismic data, mud inversion seismic data, and well drilling data were used to elucidate the lateral variations and combinations of fillings. Key coring wells were selected, and cores were calibrated using logging data on acoustic time difference (AC), density (DEN), deep-shallow dual lateral resistivity (RD-RS), natural gamma ray (GR), and shale content (Vsh). A range of quantitative benchmarks were thus established to distinguish between various types of fillings. Discrimination between breakdown breccia and calcite fillings was achieved using AC-DEN crossplots. The former exhibited elevated DEN values (2.64–2.72) coupled with moderate AC values (>49.5). Conversely, the latter displayed higher DEN values (2.66–2.76) and lower AC values (<49.5). Mechanical components and unfilled or low-filled components were identified using GR-RS or △R-Vsh crossplots, where △R signified the absolute difference between deep and shallow resistivity measurements, with a GR value of 20 API and a Vsh value of 5% within these plots representing the boundary between the two. The filling characteristics of the underground river fillings, and the mechanisms underlying the formation of these fillings were explained. A comparative analysis of the channels during different geological epochs revealed the following: (i) Sandstone and sandstone-cemented breakdown breccia that were primarily filled with a combination of mechanical and collapse fillings developed in the doline. Mudstone and calcite developed in the corridor region, whereas breakdown breccia developed at the intersections of fault lines. Uncemented breakdown breccia was frequently encountered in the branches of the underground river, with calcite developed on the blind side. (ii) The top channel of the S65 underground river formed during a period of rising sea levels in the Carboniferous. The poor lateral reservoir connectivity resulted from the extensive infiltration of mud. In contrast, the bottom channel, primarily consisting of Silurian sandstone and sandstone-cemented breakdown breccia, formed during the denudation phase of the early Hercynian. This bottom channel played a significant role in the substantial oil and gas production within the underground river system.