Boundary layer transition critically affects the dynamic stability of air vehicles when re-entrying. The transition process is dynamically coupled with the air vehicle motion, potentially causing uncontrollable oscillations. Previous researches mainly focused on the aerodynamic derivatives and dynamic modeling for reentry body oscillations. However, the interactions between free oscillations and boundary layer transition remain largely unexplored. The hypersonic transition flow past a free-oscillating blunt cone is investigated in this study. The unsteady Reyanolds averaged Navier-Stokes equations with a k–ω–γ transition model, coupling with rigid-body motion equations, are solved. This method enables a more accurate prediction of the oscillation history and models the coupled transition characteristics. Firstly, the transition model is validated by the transition flows past blunt cones with experimental data. And then, the free oscillation motion of a blunt cone at a Mach number of 6 with the initial angle of attack of 2 degrees is calculated and compared with the experimental data. The oscillation history at the beginning stage is shown below, and the numerical results agree well with the experimental data. The oscillation period and the static and dynamic aerodynamic derivatives are analyzed and compared with the experimental data. The results with transition effects are more accurate than the full turbulence model, reducing the relative error of period from 6.05% to 3.13%. Finally, the influence of moment of inertia Iy is investigated. As Iy decreases, the transition becomes more significant and the transition delay effect is strengthened.