Physical model tests were performed to discuss the causes of vortices at the intake of short culvert conveyance system of the shiplock at Xinglong hydro-junction. Effects of the operating mode of the water valve, the submerged water depth at the intake, and the intake shape and solid boundary conditions on the vortex pattern were analyzed. By comparing a series of model tests, measures of properly increasing the submerged water depth at the intake while setting vortex plate at the top of the intake were finally proposed to eliminate the air-inhaling vortices. It provided basis for the optimal design and operation management and could be referential for the design of alike projects.