Based on detailed researches on the species, abundances, crystal morphological features and stable C, O, S isotopes of the authigenic minerals in shallow core sediments of Site 5B and Site 4B within Shenhu area gas-hydrate potential deposits of northern South China Sea, the authors found that authigenic pyrites and carbonates are the dominating species in shallow sediments, and that great differences exist between Site 5B and Site 4B in abundance, distribution, morphology and grain size of pyrites and carbonates. Taking into account the same geological background of both sites in Shenhu area, the authors have inferred that the great differences might be related to the local methane flux and deep structures in different sites. Authigenic pyrites might have been formed by the anaerobic oxidation of methane or organic matter with sulfate reduction. Extremely negative sulfur isotope of pyrites might be related to the co-action of sulfate reduction bacteria and sulfur disproportionate bacteria. Authigenic carbonate was probably formed in a relatively complicated process, and carbon isotopic records might reflect mixed carbon sources of methane, organic matter and sea water.