Abstract: A variety of complicated flow phenomena such as shock wave, boundary layer, flow separation, rarefied gas effects and real gas effects exist in the flows over hypersonic flight vehicles. The hypersonic boundary layer transition is not only a basic aerodynamics issue, but also a hot topic and challenging subject in the research of hypersonic flows. The accurate prediction and the effective control of boundary layer transition can achieve meticulous design of aerodynamic force and heating, thus improving the vehicle performance and enhancing the mission capability. In this paper, the research progress in typical instability characteristics commonly existed in the flight vehicles with complex configurations in engineering is reviewed, and the complicated issues of boundary layer transition in engineering practice which are urgent to be solved are proposed. Meanwhile, the engineering application direction of the research on hypersonic boundary layer transition is specified. Moreover, the investigations on flow control of hypersonic boundary layer are reviewed in order to realize the boundary layer control in the design of hypersonic vehicle in future to enhance the flight performance.