As a kind of water storage unit, especially a large water-carrying lake, the lake is a typical plain reservoir. It has many similarities with the valley reservoir in function. However, due to its special geographical topography, the flood processes of the lake have a big difference compared with the valley reservoir. For valley reservoirs, the dam site flood which is the whole reservoir inflow flood is concerned in the flood control safety design. However, for lakes, more attention should be paid to the flood processes of each sub-region, which plays an important role in the lake area flood evolution. In this paper, according to the flood process characteristics of large water-carrying lakes, Copula function is used to construct multiple joint distribution functions, and the method that figures up the confidence interval of each sub-region flood process based on the whole flood process is proposed accordingly. Taking Lake Hongze as an example, the results show that: 1) If the joint return period is known, this method can determine the 95% confidence interval of the flood volume and flood peak of the whole flood process; 2) The rivers entering Lake Hongze were merged and clustered by runoff correlation analysis, which not only considers the natural hydrological and hydraulic connections between the rivers, but also avoids the problem of excessively high dimensions of the joint distribution function; 3) When the whole flood volume is confirmed, this method can determine the 95% confidence interval for the flood volume allocation. This method has a strong statistical and theoretical foundation and expands the application range of multivariable flood frequency analysis technology in the practice of water conservancy projects.