Wind tunnel experiments were conducted to investigate the effect of vortex generators on a transonic corner flow separation, resulting from the interaction of a normal shock wave with a turbulent boundary layer in a duct at M = 1.4. The shape of the vortex generators was rectangular. The vortex generators were mounted on the bottom wall of the test section. The investigation studied the effects of the rotation direction of the vortex, the VG size and position relative to the shock and the walls. When the leading edge of the vortex generators turn towards the corner, the effect of the vortex generators on the corner flow separation monotonically decreased as the vortex generators size reduced. In these cases, it was observed that independent separations appeared on the bottom wall. When the leading edge of the vortex generators points in the opposite direction away from the corner, the flow structure was found to depend on the size and the location of the vortex generators. We categorized the flow structures into three modes. The effect of the vortex generators and the three modes were successfully collapsed with a location parameter normalized by the second power of the non- dimensional size.