The northern margin of South China Sea contains several favorable areas for occurrence of gas hydrate. In this study, we collected pore water samples in two piston cores (X-01 and D-01) from Xisha Trough and Dongsha area, respectively, and the concentrations of sulfate and carbon isotopic compositions of dissolved inorganic carbon (DIC) were measured. The results showed different geochemical characteristics in these two sites. The X-01 core shows relatively constant δ13C-DIC values and sulfate concentrations, which suggest that anaerobic methane oxidation (AMO) processes did not occur in this site. In contrast, very large variation in δ13C-DIC values and sulfate concentrations are revealed in D-01 core, and good linear correlations for sulfate gradients and δ13C-DIC values are observed. The calculated sulfate-methane interface (SMI) depth is 9.6 mbsf. These data indicate that an AMO process occurred in sediments with large methane flux from depth in the Dongsha area, which are comparable to other gas hydrate locations in the world oceans such as the Blake Ridge. We suggest that the Dongsha area is one of the most favorable targets for future gas hydrate exploration.