A shock wave/boundary layer interaction (SWBLI) is a common phenomenon in supersonic inlet flow, which can significantly degrade the aerodynamic performance of the inlet by inducing boundary layer separation. To address this issue, in this paper, we propose the use of a dynamic vortex generator to control the SWBLI in a typical supersonic inlet. The unsteady simulation method based on dynamic grid technology was employed to verify the effectiveness of the proposed method of control and investigate its mechanism. The results showed that, in a duct of finite width at the inlet, the SWBLI generated complex three-dimensional (3D) flow structures with remarkable swirling properties. At the same time, vortex pairs were generated close to the side wall as a result of its presence, and this led to the intensification of transverse flow and, in turn, the formation of a complex 3D structure of the flow of the separation bubble. The dynamic vortex generator induced oscillations of variable intensity in the vortex system in the supersonic boundary layer that enhanced the mixing between the boundary layer flow and the mainstream. Meanwhile, the unique effects of “extrusion” and “suction” in the oscillation process continued to charge the airflow, and the distribution of velocity in the boundary layer significantly improved. As the oscillation frequency of the vortex generator increased, its charging effect on low-velocity flow in the boundary layer increased, and its control effect on the flow field of the SWBLI became more pronounced. The proposed method of control reduced the length of the separation bubble by 31.76% and increased the total pressure recovery coefficient at the inlet by 6.4% compared to the values in the absence of control.