Abstract: The Middle Route of South to North Water Diversion Project officially started large-flow water diversion in 2020. During this period, it was found that the flow pattern at inlets and exits of some conveyance aqueduct were disordered, the water level in the aqueduct fluctuated abnormally, and the diversion capacity was reduced. Taking Lihe aqueduct as the research object, high precision three-dimensional hydrodynamic numerical model was used to simulate the current flow abnormal phenomenon in Lihe aqueduct. The middle pier at aqueduct exit was relatively flat, which caused water flow sharply around and the Carmen vortex street phenomenon appeared. Pier tail flow swang periodicly causing periodic change of the two streams flow, which in turn increased the swing of the pier tail flow. The two flows motivated each other to form resonance, and enlarged the abnormal fluctuation of the water level. Combined with the actual engineering, different kinds of feasible flow regime optimization engineering measures were put forward. After numerical simualtion analysis, the most suitable engineering measures for the Lihe aqueduct were obtained, namely constructing triangular diversion piers at the upstream and downstream of the middle pier at the aqueduct entrance and exit. Considering the engineering cost performance and structural stability, it is recommended to adopt the size scheme of inlet length 10 m+outlet length 30 m. The research results can provide a reference for the flow regime improvement in the aqueduct of similar water diversion projects.