Anaerobic oxidation of methane (AOM) is a common biochemical process in the ocean and it plays an important role in global climate change, elemental circulation, and atmospheric evolution over geological time. In this paper, we analyzed of δ34S, Fe, Mn, Ca/Ti, and Sr/Ti ratios, and the date of carbon and sulfur from the site SH3 of Shenhu area. Result showed that (1) 0–6 mbsf (meter blow the sea floor) was mainly affected by OSR (anaerobic oxidation of organic matters) and 7–15 mbsf was a paleo-SMTZ (sulfate–methane transition zone) position. The modern SMTZ was mainly distributed at 19–25 mbsf. The barium sulfate precipitation above the modern SMTZ indicating that the current methane leakage was stable and lasted longer during geological history. (2) By studying the change of magnetic and the different carbonate minerals, results showed that there were two AOM stages. During the early stage, Fe2+ were mainly produced by sulfide abiotic reductive dissolution. During the later stage, Fe2+ were mainly produced by the metal-AOM. (3) Study of the mineral characteristics of the paleo-SMTZ and the modern SMTZ showed that the modern SMTZ carbonate minerals were mainly low-Mg calcite and aragonite, while the paleo-SMTZ carbon minerals were mainly high Mg minerals. The reason for this difference is that the modern SMTZ layer was only experienced the first stage of anaerobic oxidation of methane. In the paleo-SMTZ layer, it has experienced two stage of anaerobic oxidation of methane. During the last stage of metal-AOM, the low Mg carbonate minerals were converted into high Mg carbonate minerals. This research confirms the presence of metal-driven methane anaerobic oxidation at the bottom of sulfate-driven methane anaerobic oxidation and during the metal-driven methane anaerobic oxidation, methane and metal oxides or hydroxides would couple to convert the in situ metal oxides or hydroxides into metal ions, meanwhile the phosphorus adsorbed on the surface of the metal oxides is released into adjacent pore water, and convert to new P-bearing minerals under suitable conditions.