To investigate the characteristics of flood encounters between the main stream of the lower Yangtze River and Poyang Lake, based on the discharge series (from 1950 to 2023) from important hydrological stations on the lower Yangtze River (Jiujiang Station and Datong Station) and the inflow control station of Poyang Lake (Hukou Station), the ordered clustering analysis method was used to identify the mutation point (2003) of the annual total runoff and annual maximum flood peak discharge in the lower Yangtze River. Using the annual maximum flood peak discharge, annual maximum 7-day flood volume, and annual maximum 15-day flood volume as characteristic parameters of the annual maximum flood, the mixed von Mises distribution and the P-Ⅲ distribution were used to fit the marginal distributions of the annual maximum flood occurrence time and magnitude at the three stations, respectively. A two-dimensional Archimedean Copula function was employed to construct the two-dimensional joint distributions of the annual maximum flood occurrence time and magnitude in the lower Yangtze River. Based on this, the encounter risks and changing characteristics of flood occurrence time and magnitude in the lower Yangtze River before and after the impoundment of the Three Gorges Reservoir were analyzed. The results show that after the impoundment of the Three Gorges Reservoir, the encounter risk of annual maximum flood occurrence time in the lower Yangtze River increased in some aspects and decreased in others. Currently, the encounter risk of flood occurrence time between Hukou Station and the main stream stations (Jiujiang Station and Datong Station) reaches its maximum from early June to early July, while the encounter risk between Jiujiang Station and Datong Station reaches its maximum from late June to late July, which should be paid special attention to. After the impoundment of the Three Gorges Reservoir, the risk rate of encountering a certain magnitude of flood at any two stations decreased. The operation of the Three Gorges Project effectively reduces the risk of encounter in the annual maximum flood magnitude between the main stream of the lower Yangtze River and Poyang Lake, with the greatest risk reduction observed between Jiujiang Station and Datong Station.