Flow separation is mostly an undesirable phenomenon and boundary layer control is an important technique for flow separation problems on airfoils and in diffusers. The vortex generator jet method is an active control technique which provides a time-varying control action to optimize performance under a wide range of flow conditions because the strength of longitudinal vortices can be adjusted by varying the jet speed. In this study, an adaptive separation control system using vortex generator jets with rectangular orifices has been developed. The separation control system can be practically applied to the flow separation control of a two-dimensional diffuser. It was confirmed that our separation control system could adaptively suppress flow separation for the flow fields caused by some changes in freestream velocity and the divergence angle of the diffuser. Furthermore, our system has the ability to operate just before the onset of separation.