Methane hydrate in the South China Sea (SCS) has extensively been considered to be biogenic on the basis of its δ¹³C and δD values. Although previous efforts have greatly been made, the contribution of thermogenic oil/gas has still been underestimated. In this study, biomarkers and porewater geochemical parameters in hydrate-free and hydrate-bearing sediments in the Taixinan Basin, the SCS have been measured for evaluating the contribution of petroleum hydrocarbons to the formation of hydrate deposits via a comparative study of their source inputs of organic matters, environmental conditions, and microbial activities. The results reveal the occurrence of C₁₄–C₁₆ branched saturated fatty acids (bSFAs) with relatively high concentrations from sulfate-reducing bacteria (SRBs) in hydrate-bearing sediments in comparison with hydrate-free sediments, which is in accord with the positive δ¹³C values of dissolved inorganic carbon (DIC), increasing methane concentrations, decreasing alkalinity, and concentration fluctuation of ions (Cl⁻, Br⁻, SO₄²⁻, Ca²⁺, and Mg²⁺). These data indicate the relatively active microbial activities in hydrate-bearing sediments and coincident variations of environmental conditions. Carbon isotope compositions of bSFAs (−34.0‰ to −21.2‰), n-alkanes (−34.5‰ to −29.3‰), and methane (−70.7‰ to −69.9‰) jointly demonstrate that SRBs might thrive on a different type of organic carbon rather than methane. Combining with numerous gas/oil reservoirs and hydrocarbon migration channels in the SCS, the occurrence of unresolved complex mixtures (UCMs), odd-even predominance (OEP) values (about 1.0), and biomarker patterns suggest that petroleum hydrocarbons from deep oil/gas reservoirs are the most probable carbon source. Our new results provide significant evidence that the deep oil/gas reservoirs may make a contribution to the formation of methane hydrate deposits in the SCS.