In hydrological research, flood events can be analyzed by flood hydrograph coincidence. Existing flood hydrograph coincidence research mostly focuses on the analysis of the coincidence risk probability of the annual maximum flood event using the 15-day maximum annual flood volume; the actual duration of the flood hydrograph is neglected. The duration of the flood hydrograph is a key variable in (1) determining whether flood hydrograph coincidence occurs, and (2) accurately calculating the flood hydrograph coincidence risk probability. 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, using 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. The flood hydrograph coincidence volume-risk probability curve was also obtained, providing 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.