The selection of an appropriate turbulence/transition model is critical when simulating the hypersonic flows based on the Reynolds-averaged Navier–Stokes (RANS) equation. In particular, a deep understanding of the validity, reliability, and limitations of existing models is an essential prerequisite to facilitate their further development. This paper reports on the assessment of two models dedicated to hypersonic boundary layer transition analysis. Both models are compared with two other models that are widely used in this field. The double ramp and shock wave laboratory scramjet intake cases are used for the validation and evaluation of the predictive performance of both models via comparison against experimental data. The results reveal that the appropriate selection of the transition model is critical to the attainment of accurate results. Moreover, the forebody of the scramjet combustion propulsion-01 (SCP-01) flight vehicle, which is a research model, is analyzed as a case study. The air intake performance of the SCP-01, as predicted by four models, is compared and analyzed at different flight altitude and Mach number conditions. The results reveal that the accuracy of the prediction of boundary layer and separated flow transitions significantly affects the flow field and corresponding air intake performance. Furthermore, the uncertainty of results obtained using the two models increases significantly with an increase in altitude. Finally, the reliability and limitations of the transition models considered in this study are examined.