Recent occurrence of Peridiniopsis blooms has become a routine phenomenon in the tributaries of the Three Gorges Reservoir, however the mechanism under them is still unknown. In the present study, ecological surveys on phytoplankton were intensively performed in the Peridiniopsis blooms occurring Tongzhuang River, then extending to the main stem of the Yangtze River and 26 tributaries in Three Gorges Reservoir during 2009 to 2011. The results showed that the occurring frequency, average and maximum densities, and maximum dominance of Peridiniopsis sp. were highest in backwater areas of the tributaries in April. During February to April, the density of Peridiniopsis sp. had a pattern with initial increase and later decreased at each sites in backwater area of Tongzhuang River, and the highest density of Peridiniopsis sp. dramatically decreased from the upstream to the downstream. In 2010, Peridiniopsis bloom firstly occurred in the upstream of backwater area of Tongzhuang River in February, gradually developed into the downstream, and disappeared after a long duration. The occurring frequency, density, and maximum dominance of Peridiniopsis sp. in main stem of Yangtze River were far lower than those in backwater area of Tongzhuang River on the same seasons. Compared with the year without occurrence of Peridiniopsis bloom, the years with Peridiniopsis blooms were characterized with lower daily water discharge out of the Three Gorge Reservoir (average values range from 4489.9 to 5623.3 m³/s) from January to March, and with higher daily water level amplitude in January (average value is 0.148 m) and February (average value is 0.246 m) and daily water level lift (average value is -0.223 m). The results demonstrated that water temperature in backwater area of tributaries from February to April was optimal to the occurrence of the Peridiniopsis blooms, indicating the importance of water temperature triggering the blooms. The nitrogen and phosphorus levels were shown to meet the capability of nutrient and life habit of Peridiniopsis sp.. It was concluded that formation of Peridiniopsis blooms in the Three Gorges Reservoir should depend on the following conditions: hydrodynamic conditions in upstream of backwater area, hydrological conditions such as water discharge out of Three Gorges Reservoir and water level variation by changing flow rates in backwater area and hydrodynamic conditions in its upstream to influence the occurrence, timing, extent, scale and duration time of the blooms. Due to the effects by the different scales, the influence of same hydrological conditions of the Three Gorges Reservoir on occurrence of Peridiniopsis blooms at different sites were not the same.