In open-channel water transfer projects, hydrodynamic modeling has been one of the tools commonly used by the scheduling staff to perceive the changes in the water condition of the channel. The reliability of the flow monitoring data has not been guaranteed due to restrictions in the flow monitoring method. Flow monitoring errors directly reduce the accuracy of hydrodynamic modeling calculations, making it impossible to accurately grasp the real-time changes in the internal water conditions of the channel. In this paper, by utilizing the characteristics of the hydrodynamic model itself, which can be solved discretely with multiple boundary conditions, the method of correcting the boundary anomaly data is proposed by changing the combination of hydrodynamic boundaries. This solves the problem of the inaccuracy of hydrodynamic model calculations due to errors in the monitoring data and improves the accuracy of the hydrodynamic model calculations. In the actual operation process, it is found that the method proposed in this paper solves the problem of hydrodynamic model misalignment caused by flow observation errors by correcting the flow during the flow adjustment period, which greatly improves the calculation accuracy of the hydrodynamic model. Secondly, for a stable flow period, the method proposed in this paper can quickly capture and correct the local monitoring of abnormal data and improve the overall hydrodynamic simulation accuracy.