Abnormal large water waves with amplitudes up to 1.0 meter were observed under large discharge conditions in the Shierlihe aqueduct, part of the main canal of the South-to-North Water Diversion Middle Route Project. Due to the large water waves, the water conveyance capability of the main canal is affected, and associated structures are endangered. Hydraulic model tests were carried out to reproduce the abnormal water waves observed in the prototype aqueduct. Result reveals that the alternative change of inflow between the left and right ducts induced by Karman vortex street at the exit of the aqueduct is the major cause of abnormal water waves with large amplitudes in the aqueduct. By eliminating the wave source, i.e., Karman vortex street at the exit pier of the aqueduct and preventing the alternative change of inflow conditions in the left and right ducts at the aqueduct entrance, engineering measures and scheduled gate operation scheme are proposed to reduce the abnormal water waves in the aqueduct. It is found that the maximum wave amplitudes in the aqueduct can be reduced to below 0.2 meter under all discharge conditions. The proposed gate operation strategy has been applied to the prototype project, and the abnormal water waves in the aqueduct and canal are well controlled.