Based on the data of daily precipitation of 271 meteorological stations in the upper reaches of the Yangtze River and the data of the Three Gorges Reservoir inflows during 1961-2017, this study analyzed the influence of precipitation in the upper reaches of the Yangtze River on the inflow of the Three Gorges Reservoir by using t-test, synthetic analysis, correlation analysis, and cluster analysis. The results show that: 1) The precipitation in August and September has the greatest influence on the key monthly inflow of the Three Gorges Reservoir. 2) According to the precipitation characteristics, the upper reaches of the Yangtze River can be divided into six zones, in which the regions along and in the south of the Yangtze River is divided based on the natural watersheds: Zone I (the south of the Jialing River), Zone II (the upper reaches of the Jinsha River, the north of the Mintuojiang River, and the north of the Jialing River), Zone III (Chongqing-Yichang), Zone IV (the Wu River), Zone V (Yibin-Chongqing), and Zone VI (the middle and lower reaches of the Jinsha River). 3) The contributions of the six zones to the key monthly inflow of the Three Gorges Reservoir are as follow: with the largest precipitation and the shortest catchment distance, Zone I and Zone III have the greatest contribution in these six zones; Zone II has sparse and unevenly distributed stations, and due to the lowest precipitation and longest catchment distance, it makes the least contribution; and the remaining three zones (Zone IV, V, and VI ) make similar contributions. 4) The analysis on the three great floods with peak flow over 50000 m³/s since the Three Gorges Reservoir began to fill in 2003 finds that the continuous heavy precipitation in Zone I during 11 to 18 September 2014 and the intermittent heavy precipitation in Zone III were the root causes for the occurrence of the super food with peak flow exceeding 50000 m³/s. It also proves that the result drawn by analyzing the influence of the contribution of the precipitation in Zone I and Zone III is reliable and can provide references for the rational dispatching of water storage in the Three Gorges Reservoir.