Taking the control basin of the Kenswat hydrological station of the Manas River as the study area, considering the frequency structure characteristics under variation conditions, the joint distribution of flood peaks and flood volumes was established based on Copula function, and the risk probability under the interaction between each flood peak and flood volume was calculated to build the risk assessment model. The results show that the mixed distribution can better reflect the frequency distribution of flood variables under the condition of variation. The flood combination characteristics can be well described by the joint distribution of flood peak and flood volume based on Gumbel Copula function. Under the 500-year flood control design standard of the Manas River flood peak and flood volume, the joint risk and co-occurrence risk both reach the minimum value, and the probability of flood occurrence is low. Therefore, the design standard of flood peak and flood volume with relatively close frequency can not only ensure the low risk rate of flood occurrence, but also meet the actual needs of project hazards.