More and more attention has been paid to the study of the impact of extreme climatic events on the ecological environment off the Changjiang River Estuary. In this study, the relationship between the chlorophyll concentration and ENSO (El Niño Southern Oscillation) events was studied. Several potential physical mechanisms between the ENSO and chlorophyll concentration were analyzed using observation and sensitivity experiments from a high-resolution ROMS-CoSiNE coupled model (Regional Ocean Modeling System-Carbon, Oxygen, Silicon, Nitrogen and Ecosystem) off the Changjiang River Estuary. Our results indicated that the April to August averaged chlorophyll concentration off the Changjiang River Estuary was significantly correlated with the December to February averaged ENSO indices in the previous winter. The 10 m wind speed and SST (Sea Surface Temperature) affected by an ENSO event had little effect on the chlorophyll concentration, while the discharge had a significant effect on the chlorophyll concentration off the Changjiang River Estuary, and the discharge was significantly and positively correlated with the ENSO indices. We tested the effect of interannual variations of the discharge and nutrients carried by discharge on the interannual variation in the chlorophyll concentration in the ENSO events. Two sensitivity experiments showed that when the nutrients in the freshwater discharge were kept as a constant seasonal cycle, the composite differences in the chlorophyll concentration between the positive and negative ENSO phases off the Changjiang River Estuary were reduced. When there were no nutrients in the freshwater discharge, the composite differences in the chlorophyll concentration between the positive and negative ENSO phases off the Changjiang River Estuary were reduced by one order of magnitude. The discharge can modify the stratification off the Changjiang River Estuary, and the nutrients carried by the discharge play a dominant role in determining the interannual variation of the chlorophyll concentration associated with the ENSO cycles.