In order to analyze the influence of rainfall seepage on the stability of cofferdam, focusing on an navigation-powered junction project in Jiangxi Province, based on the unsaturated seepage theory, this study simulates and explores condition of the seepage and the stability of cofferdam under different rainfall conditions by using the Geo-studio numerical simulation software, and the influence of different rain patterns on the stability of cofferdam is obtained. The results show that the influence of rainfall on the cofferdam has a hysteretic quality. The influence of different rainfall types on the strength hysteresis of weir body is as follows: rear peak type, uniform type, middle peak type and front peak type, and the hysteresis are affected by rainfall intensity. The rainfall infiltration is affected by the time of the peak rainfall, and the safety factor of the cofferdam decreases sharply with the peak rainfall intensity. Compared with the initial stability conditions, the front peak type rainfall has the least impact on the stability of the cofferdam, and the rear peak rainfall has the greatest impact on the stability of the cofferdam. Under the influence of early rainfall, the permeability coefficient of soil in the slope would be at a high level. Thus, the ability of cofferdam to resist sudden heavy rainfall weakens with the increase of permeability coefficient.