Based on the ECOM-si, a physical-ecological coupled numerical ocean model off the Changjiang Estuary with modules of circulation, thermohaline, sediment simulation and NPZD type of ecological model was established.The model was validated by observed data of several sites and sections, and the simulated results show a certain precision and stability.Therefore, the model can be applied to seasonal variation study of the phytoplankton biomass off the Changjiang Estuary, and the influences of increase-decrease of water discharge in different months and during high, normal and low flow years, on the nutrients and the monthly mean biomass of the phytoplankton,after the runoff of Changjiang regulated by Three Gorges Project(TGP). The modeling results showed that, the absolute value of nutrients variation was decreased from the nearly estuary to the far estuary,and the peak value of nutrients variation occurred successively from west to east. Low flow year was influenced greatly by runoff regulation, and the nutrients increment during low flow year was significantly greater than during high and mean years caused by runoff regulation in the estuary, while the nutrients decrement was on the contrary in the transition area and the far estuary after October.The distribution of phytoplankton biomass was relatively consist with that of nutrients, with a greatest effect during the low flow year andthe peak value also occurred successively from west to east.In addition, due to the competition between diatoms and dinoflagellates, the increased absolute amplitude of diatom biomass in flow increased season was higher than the decreased amplitude of diatom biomass in flow reduced season, while dinoflagellates was on the contrary.Runoff regulation of TGP was beneficial to the growth of phytoplankton off the Changjiang Estuary, but the annual mean increased biomass was small.