Recent studies have shown that specific geochemical characteristics of sediments can be used to reconstruct past methane seepage events. In this work, the correlation between the Sr/Ca and Mg/Ca ratios of sediment samples is analyzed and the sulfate concentration profile in Site C14 from cold-seep sediments in the Qiongdongnan Basin in northern South China Sea is obtained. The results confirmed that, sulfate at 0–247 cm below sea floor (Unit I) is mainly consumed by organic matter sulfate reduction (OSR), while sulfate at 247–655 cm (Unit II) is consumed by both the OSR and the anaerobic oxidation of methane (AOM). In addition, the bottom sediment layer is affected by weak methane seepage. The Mo and U enrichment factors also exhibit similar trends in their respective depth profiles. The responses of trace elements, including Co/Al, Ni/Al, Cr/Al and Zn/Al ratios to methane seepage allowed the study of depositional conditions and methane seepage events. Based on the results, it is speculated that the depositional conditions of Unit II changed with depth from moderate conditions of sulfidic and oxic conditions to locally anoxic conditions, and finally to suboxic conditions due to methane fluid leakage. The stable isotope values of chromium-reducible sulfide produced by AOM and those of sulfide formed by OSR in the early diagenetic environment suffered serious depletion of 34S. This was probably due to weak methane leakage, which caused the slower upward diffusion and the effect of early diagenesis on the samples. It is necessary to consider the effects of depositional environments and diagenesis on these geochemical parameters.