Abstract: The flight environment of high-speed aircraft is relatively complex, and the reliability of numerical simulation results of this process can be affected by the freestream condition variation. In order to assess and quantify the aerodynamic and aerothermodynamics uncertainty of high-speed aircraft due to the freestream variation, a double ellipsoidal configuration featuring the combination of a front fuselage and a cockpit cover of the space shuttle was selected as the research model, and the numerical simulation approach was adopted to obtain the flow structures, wall heat flux, pressure distributions and other characteristics. The reliability of the prediction method was verified by comparing the simulation results with the experimental data, which demonstrated the reliability of the prediction method. Based on the Latin hypercube experimental design method and the non-intrusive polynomial chaos expansion method, the freestream density, freestream temperature, wall temperature, and freestream velocity were selected as the uncertainty input variables, and the uncertainty quantification and sensitivity analysis on the aerodynamics and aerothermodynamics of the double ellipsoid model were conducted. The research results indicate that, the uncertainty of freestream conditions has a significant impact on the lift, drag, and stagnation heat flux values of the double ellipsoid model. Variations in the freestream velocity and temperature significantly affects the wall pressure distribution, while variations in the freestream velocity, freestream density, and wall temperature strongly affect the wall heat-flux prediction.