Cold-water corals (CWCs) are frequently found at cold seep areas. However, the relationship between fluid seepage and CWC development is not clear. Here, for the first time, we report the occurrences, species identification, mineralogy, carbon and oxygen isotopes, as well as elemental compositions of fossil CWC skeletons from gas-hydrate-bearing sediment in drilling cores from the South China Sea (SCS). Three sites (GMGS-08, GMGS-09B, and GMGS-16) were investigated but CWCs were only found at one site (GMGS-09B). Interestingly, the CWCs were found in three horizons and they were all embedded with authigenic carbonates. Three genera of fossil CWCs (Crispatotrochus sp., Solenosmilia sp. and Enallopsammia sp.) were identified. The CWC fragments are predominantly aragonite. The CWCs exhibit δ13C values between −8.4‰ and −0.6‰ that are significantly higher than δ13C values of the associated seep carbonates (δ13C values with an average of −55.6‰, n = 19), which indicates a carbon source other than methane for the CWCs. It appears that authigenic carbonates provide a substratum for coral colonization. Bathymetric high points, appropriate water temperature and stronger bottom-water currents at site GMGS-09B might be crucial to keep conditions favorable for the growth of CWCs in the studied area. In addition, high trace-element concentrations of Cr, Ni, Pb, U, Ba, Th, and Sr suggest that the CWCs are influenced by strong fluid seepage that can reach the water-sediment interface, and associated microbial activity. Hence, it also becomes evident that CWCs in hydrocarbon-rich seepage areas not only provide a critical constraint on the impact of fluid emission on the bottom water chemistry, but also are likely to be very precise recorders of the end time of cold seep activity.