Abstract: To mitigate abnormal flow patterns, such as significant water level fluctuations, turbulence, and eddy currents in high-flow scenarios, a hydraulic model experiment and three-dimensional numerical simulation were conducted using a typical double-hole aqueduct model. The aim was to investigate the wave surge phenomenon caused by the Karman vortex street at the aqueduct’s outlet when constrained by the boundary. By employing both physical model experimentation and numerical simulation, a “spindle type” diversion pier concept was developed based on the observed mechanism. The study revealed a consistent shedding frequency between the Karman vortex street and the upstream surge wave frequency. Under boundary constraints, the Karman vortex street’s alternating shedding generated transverse alternating forces. These forces, combined with localized water blockages, induced wave transmission to the upstream region. Consequently, the upstream wave exhibited alternating patterns in response to the vortex street’s shedding. Implementing the “spindle type” diversion pier resulted in improved flow patterns at the inlet and outlet, significantly reducing the strength of the vortex street and its impact on the upstream flow pattern. Notably, the maximum amplitude reduction of the trough body exceeded 80%. Based on the results from a comparative test involving different lengths of diversion piers, the combination that offers the optimal balance between performance and cost-effectiveness is recommended. This combination consists of inlet and outlet diversion piers with an aspect ratio A_R=L/W of 1.5, 2.0, respectively.