The decreased performance of the waterjet pump and the thruster is mainly caused by the inlet flow distortion of the waterjet pump due to the flow separation at the back of the inlet duct of the flush-type waterjet. A typical flush-type intake duct is selected for a waterjet based on the theory of suppressing the possible flow separation by using the vortex generator/vortex generator jet (VG/VGJ). The flow in the flush-type intake duct of the waterjet is then simulated by the blowing model test in the low-speed wind tunnel. The distributions of the static pressure on the wall of the inlet duct and the total pressure on the surface of the waterjet pump inlet were measured to explain the mechanism of promoting the propulsion performance by the VG/VGJ, obtaining the influence of the structural dimension and installation locations of the VG/VGJ on the flow control. At a low advance ratio ( IVR=0.5), the properly installed VG/VGJ can improve the total pressure recovery coefficient of the inlet duct and the uniformity of the axial velocity of the waterjet pump inlet surface, resulting in an increase of thrust about 5%.