The Shenhu hydrate reservoirs of northern South China Sea are speculated to form and accumulate under the free gas-rich environment, and accord with the flow-transportation-reaction process. During this process, the area has also experienced simultaneous alternations of the local geological structures and ambient environmental conditions. First-order reaction kinetics, which controls the hydrate reaction, is coupled with the seafloor sedimentation to quest the dynamic formation and aggregation mechanism of the Shenhu hydrate layers. Firstly, based on the indications from Peclet number, the hydrate reaction shall play more active roles during the natural sedimentation in this process. Secondly, when the average seafloor sedimentation rate and the initial seafloor were 5 cm/ka and 988 m, respectively, three moments (50 ka, 3 Ma, and 5 Ma) are chosen to investigate the evolution process of the hydrate reservoirs and exhibit the change of the local pressures, temperatures, dissolved methane and salt, phase saturations, stratum permeability, and pore capillary pressure. The results show that after 5 Ma the occurrence and distribution of hydrate-bearing sediments proceed to be nearly consistent with the current status. Finally, the effects of five factors, including methane flux, kinetic coefficient, initial fluid position, permeability and seafloor sedimentation rate which simultaneously control the accumulation together in this zone, are quantitatively discussed. It verifies that the reaction-sedimentation mechanism is applicable for researching the Shenhu hydrate system. Under this model it should have a small methane flux and relatively small reaction coefficient here.