Despite many studies on seafloor hydrothermal systems conducted to date, the generation mechanism of seafloor massive sulfide (SMS) deposits is not yet fully understood. To elucidate this mechanism, this study clarifies the three-dimensional regional temperature distribution and fluid flow of a seafloor hydrothermal system of the Iheya North, middle Okinawa Trough. Lateral flow and boiling of hydrothermal fluids below the seafloor were the main features found by the simulation, leading to an interpretation of two-layered SMS deposit generation as follows. Hydrothermal fluids discharging from black smokers first formed the upper SMS deposits on the seafloor. Caprocks formed below the seafloor, and the above-mentioned occurrences were then induced under the caprocks. In the present system, vapor-rich hydrothermal fluids poor in metals are discharged from the vents as white smokers, whereas liquid-dominated hydrothermal fluids rich in metals flow laterally below the caprocks, forming lower SMS deposits tens of meters below the seafloor.