Abstract Hypersonic boundary layer transition is a hot yet challenging problem restricting the development and breakthrough of hypersonic aerodynamics. In recent years, despite great progress made by wind tunnel experiment, transition mechanism and transition prediction, only partial knowledge has been gained so far. In this paper, firstly, the specific scenarios of hypersonic boundary layer transition control are clarified. Secondly, the experimental research progress and mechanism of passive control and active control methods under different hypersonic transition control demands are summarized, with their advantages and disadvantages being analyzed separately. Plasma actuation is easy to produce controllable broadband aerodynamic actuation, which has potential in the field of boundary layer transition control. Hence, the following part of the paper focuses on plasma flow control. The feasibility of plasma actuation to control the hypersonic boundary layer transition is demonstrated and the research ideas are presented. Finally, hypersonic boundary layer transition control methods are summarized and the direction of future research is prospected.