Abstract: The laminar-to-turbulent transition of boundary layers is crucial for the aerodynamic and aerothermal design of high-speed vehicles as it results in a significant increase in skin friction and wall heat flux. In high-enthalpy boundary layers, the transition process becomes even more intricate due to various thermo-chemical processes induced by the extremely high temperature. This study employs chemical non-equilibrium linear stability analysis with 5-species and 11-species atmospheric models to investigate blunt cone boundary layers under reentry conditions, focusing on the effects of Mach number and ionization on the boundary-layer stability. The results indicate that the transport coefficients of ionized air calculated using the Gupta-Wilke (GW) model exhibit significant errors. In contrast, the results of the GW model without considering electrons are more aligned with those of the Chapman-Enskog (CE) model. Under flight conditions, as the Mach number increases, the growth rate of the second mode decreases gradually, while the instability frequency range broadens. Ionization primarily affects the base flow near the nose. Specifically, ionization at the nose slightly reduces the growth rate of the second mode upstream but does not alter the overall N-factor, thereby having a negligible effect on the aircraft's transition prediction. Additionally, the computational efficiency of real-gas transition predictions can be improved by using a five-species model.