The hydraulic engineering built at the inflow into the junction can be affected by both main and tributary floods. The control flood level has relationship not only with flood combination characteristic, but also with the coupling relation between flood and hydraulic engineering flood discharge. The existing methods of designed flood level assessment, based on the characteristic flood combination corresponding to the design flood recurrence period or the empirical combination directly, cannot accurately reflect the interaction between floods and hydraulic engineering. In this paper, the Copula-Monte Carlo simulation method is used to calculate the flood control design water level of hydraulic engineering built at the inflow into the junction. The acceptability is verified via a case study in the sluice of Guangxi Guiping Shipping Hub, Xijiang River, Pearl River Basin. The results show that, the proposed method can be used to account for the combination characteristic of main and tributary floods and coupling relationship with flood discharge of hydraulic engineering. The calculation result of the designed flood control water level meets the requirement of the flood control standard, indicating that the uncertainty of determining the designed flood control water level by using the flood return period is effectively overcame. Under the combined action of main and tributary floods, the design water level varies tremendously by using the different combinations of characteristic of the design flood recurrence period. The deviation exceeds the reasonable error range of the flood control standard, suggesting the unacceptability of the use of the design flood return period on the determination of flood control level. Otherwise, the results also indicate that it is difficult to reflect the flood and engineering characteristics of different projects reasonably by using empirical flood combination. The paper can provide a more reasonable theoretical basis and ideas for flood control design of the hydraulic engineering affecting by main and tributary floods at the inflow into the junction.