For the boundary separation and block of the scramjet inlet by the shock wave and boundary interacting, a kind of boundary control method based on the T-S wave syntony principle is presented, and the method is calibrated by the wind tunnel test for a typical 2D inlet. The results of the example showed that the boundary control method could eliminate the boundary separation efficiently, and decrease the negative influence of boundary separation, so the inlet’s capability could be maintained. The research coinstantaneous shows that the boundary transition should be considered, and effective transition method should be adopted to ensure the normal work of the scramjet engine.