The variation law of dissolved silica (DSi), dissolved inorganic nitrogen (DIN), dissolved inorganic phosphorus (DIP) and nutrition structure after the Three Gorges Project (TGP) impounding as well as their ecological effect were analyzed according to monitoring survey of the Yangtze River Estuary in spring (May) and summer (August) from 2004-2009. The results showed that after impounding, DSi and DIN concentration decreased and increased, respectively. During the study period, DSi decreased by about 63%, while DIN almost tripled. DIP concentration fluctuated slightly. With respect to nutrition structure, N:P increased, whereas Si:P and Si:N declined. According to chemometry standard of nutrient limits, nutrition structure tended to be imbalanced and the limiting factor of phytoplankton growth (P) was studied. Changes of nutrition structure have largely decreased diatom and caused different composition of dominant phytoplankton species. This may change ecosystem structure of the Yangtze River Estuary.