The transition of boundary layer flows has crucial effects on aerodynamic and heat performances of hypersonic vehicles. The fluctuation energy transport equation based on Favr? average was solved in conjunction with the Favr? averaged Navier-Stokes equations to predict the onset of the boundary layer transition. By comparing with the available experimental data, numerical results demonstrate that larger unit Reynolds number produces earlier transition, and the angle of attack delays transition on the windward surface, while promotes it on the leeward surface.