Abstract: Hypersonic boundary layer transition has become a key factor to be considered in aircraft design, and is also a hot and difficult point in hypersonic flow research. There are three typical flow structures and instability characteristics in hypersonic three-dimensional boundary layer, namely cross flow, flow direction vortex and contact line, which have different mechanisms to induce transition. Three global stability analysis methods (BiGlobal, PSE3D and TriGlobal) suitable for three-dimensional boundary layer are introduced. The structure, applicability and application of four commonly used transition models, such as the Low-Reynolds-Number turbulence model, γ-Re_θt , k-ω-γ , laminar-kinetic energy transition model, are summarized. The advantages and disadvantages of eMalik, LASTRAC, LILO, HyTEN and other transition softwares based on e^N method are analyzed. The future of transition research and software development in hypersonic three-dimensional boundary layer is prospected.