Abstract: The Three Gorges Dam was altogether finished in 2009 and water level will reach 175 meter during dry season (winter) and fall back to 145m during rainy season (summer). Impoundment of the Three Gorges Reservoir forms three significant different water types in the main stream of the Three Gorges Reservoir in Chongqing: Natural riverine zone (above 175 m) where the change of water environment fluctuate with seasons, Transition zone (145-175 m) where water environment is effected by seasons and impoundment and Analogous lacustrine zone where water level is below 145 m throughout the year. They are different in velocity of flow, nutritive level (such as the concentration of N and P) and so on. For investigating the response to these changes of algae, the physical and chemical characters of water in the main stream were tested and surveys on the phytoplankton communities in the Three Gorges Reservoir were carried out in September 2009 (time before impoundment of the Three Gorge Reservoir), January (storage period), March (drainage period) and September 2010 (time before the second impoundment). The result as follows: The mean of pH was 8.17 and Dissolved Oxygen (DO) changed from 6.54 mg/L to 11.44 mg/L during the investigation. Total nitrogen (TN) of all sample points was between 1.43 mg/L and 3.55 mg/L, and Total phosphorus (TP) was between 0.09 mg/L and 1.33 mg/L. The level of nitrogen and phosphorus nutrients were much higher than the international standard of eutrophication (0.2 mg/L and TP 0.02 mg/L) and were also a little higher than previous studies done by other researchers during initial water impoundment of reservoir. A total of 476 plankton species belonging to 7 phyla were identified, among which Bacillariphyta (63.9%) were dominant. Just like other subtropic riverine reservoirs, the Three Gorges Reservoir was full with phytoplankton in Chlorophyta and Cryptophyta during spring. algae in Cyanophyta began to increase in summer and autumn while Bacillariphyta dominated community of phytoplankton in winter. Yet different water types have changed with seasons differently: (1) with the decreasing of velocity of flow and the changes of water types from natural riverine zone to analogous lacustrine zone, the dominant species of water column changed from Bacillariphyta to Chlorophyta and the dominance degree index of Chlorophyta increased to 0.62, in the meanwhile the proportion also raised gradually and went up to 67.8% in analogous lacustrine zone in spring (March, 2010). In September, 2009, the proportion Cyanophyta increased to 52.6% and at the time of September, 2010, the proportion of Cyanophyta in phytoplankton even soar to 63.8% becoming main species. Such as Oscillatoria tenuis Ag whose dominance degree index was significant higher than any other species. Although Bacillariphyta were put one at an absolute predominance in all the water columns during winter, the abundance of algae in Chlorophyta in analogous lacustrine zone was larger than any other water types. (2) The mean Shannon-Wiener diversity index in the main stream was 2.43, and the variation in analogous lacustrine zone was in summer and autumnwinterspring. On the contrary, the index was the lowest in winter in natural riverine zone and transition zone. The evenness index changed between 0.52 and 0.85 and the evenness in spring was lower than any other seasons. Contrast previous studies, we can indicate that the water quality of he main stream of the Three Gorges Reservoir of Chongqing may become worse during these years and we should pay more attention to this trend and try to prevent it.