The impoundment of the Three Gorges Reservoir affects the changes of rainfall-runoff relationship in reservoir area, so the water resources planning of the reservoir area has to take this effect into consideration. In this paper, the measured rainfall-runoff value of 41 a (1977-2017) from Wan County Hydrological Station was selected to study the distribution of rainfall-runoff at each water storage stage, then the joint distribution function of each water storage stage was calculated using the Copula function model to quantatively analyze the effect of reservoir impoundment on its relationships, based on which the hydrological situation in this area after 2017 was predicted. Research indicates that the Copula function joint distribution mathematical model is applicable to the caculation of rainfall-runoff relationship of different stages in Wan County section of the Three Gorges Reservoir. The rainfall- runoff relationship of Wan County section of the Three Gorges Reservoir has changed greatly after it was converted from a natural river course to a part of reservoir course. At the natural river course stage, the marginal distributions of rainfall and runoff in this area were better described using Pearson III distribution. Whereas the rainfall changed to Gumbel distribution and the runoff changed to lognormal distribution during the construction period and preliminary impoundment stage. At the experimental stage, the rainfall became lognormal distribution, and the runoff returned to the Pearson III distribution. Compared to the natural river course stage, during the construction period and preliminary impoundment stage the annual rainfall decreased by 38.4%, the annual runoff decreased by 20.6%, whereas the annual rainfall increased by 24.5%, and the annual runoff decreased by 57% at the experimental stage. According to the prediction results of this mathematical model, the annual runoff of this area will be no less than 349.0×109 m3 (±5%), but no more than 405.5×109 m3 (±5%), the annual rainfall will be no less than 1 048 mm (±5%), but will not exceed 1 842 mm (±5%). This research can provide a theorectical support for the development and utilization of water resources and the reconstruction of hydrological sequences in the Wan County section of the Three Gorges Reservoir area. It can also provide some reference for the research of hydrological characteristics changes of river channels in other reservoir areas.