The hydrodynamic characteristics have changed greatly in the mainstream and its tributaries since the impoundment of Three Gorges Reservoir (TGR).Through field observation and a two-dimensional, laterally averaged, hydrodynamic model simulation by CE-QUAL-W2, we compared and analyzed the spatial and temporal distributions of the water temperature and the hydrodynamics of Shennong River bay in the TGR in different running periods. The comparative analysis results reveal that water flow has become quite slow in Shennong Bay, and density currents of different strengths exist in different running periods, including reverse density currents from mainstream to bay and the accordant bottom density current from the Shennong River to bay. In dry season and the drawdown period before flood season, the water of the mainstream of TGR flows into the Shennong Bay in surface density current with low strength; while in wet season and impoundment period in the end of flood season, mid-layer density current of high strength affects the whole bay. Downward bottom density current exists at the upstream inflow because the temperature of incoming flow is usually lower than that in the bay. Furthermore, the water temperature in the bay increases in spring and summer and decreases in autumn and winter. The stratification of water temperature is obvious in the bay in all seasons, but was weak in winter and strong in other seasons. The model of stratification is quite different from that of general reservoirs due to density currents. The simulation results indicate that CE-QUAL-W2 model performs well in simulating the density current and water temperature stratification characteristics. This research offers technical support for detailed analysis on the hydrodynamics in Shennong River of TGR.