In hydrological research, flood events can be analyzed by flood hydrograph coincidence. The duration of the flood hydrograph is a key variable to calculate the flood hydrograph coincidence risk probability and determining whether flood hydrograph coincidence occurs, while the actual duration of the flood hydrograph is neglected in most of existing related research. This paper creatively proposes a novel method to analyze the flood hydrograph coincidence risk probability by establishing a five-dimensional joint distribution of flood volumes, durations and interval time for two hydrologic stations. More specifically, taking the annual maximum flood of the upper Yangtze River and input from Dongting Lake as an example, the Pearson Type III and the mixed von Mises distributions were used to establish the marginal distribution of flood volumes, flood duration and interval time. Subsequently, the five-dimensional joint distribution based on vine copula was established to analyze the flood hydrograph coincidence risk probability. The results were verified by comparison with a historical flood sequence, which show that during 1951–2002, the hydrograph coincidence probabilities corresponding to its flood event coincidence volumes of 2.00 × 1011 m3, 4.00 × 1011 m3, and 6.00 × 1011 m3 are 0.213, 0.123, and 0.049, respectively. It has provided theoretical support for flood control safety and risk management in the middle and lower Yangtze River. This study also demonstrates the significant beneficial role of regulation by the Three Gorges Water Conservancy Project in mitigating flood risk of the Yangtze River. The hydrograph coincidence probability corresponding to its flood event coincidence volume of 2.00 × 1011 m3 has decreased by 0.141.