Based on the data from 12 representative stations on the Yangtze River Basin and Three Gorges River Basin, according to the 500year sequence of drought/flood grades and the precipitation data from May to September since the establishment of the stations, on the basis of drought/flood grade standards, the sequence of drought/flood grades is obtained for the Yangtze River Basin, the upper reaches, the middle reaches, the lower reaches of the Basin, and the Three Gorges Reservoir Area from 1470 to 2011. The results show that the reaches of Yangtze River and the Three Gorges reservoir area displayed the more significant alternating of droughts and floods, but the drought frequency accelerated in the 20th century and flood frequency increased from the 19th century. The frequencies of drought over years in the Yangtze River Basin and Three Gorges reservoir area had 160year periodic oscillation. The frequencies of flood and over in the Yangtze River Basin showed 140 years periodic oscillation, but after the 20th century the trend weakened, and that in three Gorges reservoir area had 100years periodic oscillation. The spatial and temporal distribution characteristics of precipitation were consistent with the decreasing trend, by using EOF. At the same time, the precipitation of the upper reaches of the Yangtze River had a downward trend, reflecting the drought trend of the upper reaches of the Yangtze River basin and three Gorges reservoir area. By using MK mutation test, there was no significant change in precipitation before and after the reservoir water storage in the upper reaches of the Yangtze River Basin and the Three Gorges reservoir area. In the context of global climate change, the drought evolution of the Three Gorges reservoir area is not an isolated event. It is inseparable with the background of the upper reaches of the Yangtze River and the whole basin.