A newly developed ecosystem model-the first model describing the ecological connectivity consisting of both benthic-pelagic and central bay-tidal flat ecosystem coupling while simultaneously describing the vertical micro-scale in the benthic ecosystem-was developed and applied to Tokyo Bay. The model outputs demonstrated the significant ecosystem responses as follows. First, the benthic oxygen consumption during summer was quite low due to the low level of dissolved oxygen (hypoxia), although reduced substances, Mn^<2+>, Fe^<2+>, and S^<2->, were highly produced and accumulated in the pore water. Second, both the tidal flat creation and nutrient load reduction decreased the anoxic water volume and mass of detritus in Tokyo Bay. However, the creation of tidal flats led to the higher biomass of benthic fauna, while the nutrient load reduction led to the lower biomass of benthic fauna compared to the existing situation. Lastly, in the simulation, Tokyo Bay reproducing reclaimed tidal flats (earlier Tokyo Bay system) prevented the increase of oxygen consumption potential (hypoxia potential) and the decrease of higher trophic production to red tide, compared to the existing Tokyo Bay system with reclamation of tidal flats.