The flight performance of traditional hypersonic vehicles is limited to a specified incoming flow condition, their aerodynamic performance significantly deteriorates outside of the design condition. We construct a data-driven design framework for aerodynamic shape optimization of hypersonic vehicles, which can be used to improve the current flexibility of designing hypersonic vehicles based on the existing shockwave shape or flowfield. The framework uses a class function/shape function transformation to set parameters for the control sections of the vehicle, then the dimensions of the parameter matrix are reduced by using the proper orthogonal decomposition, and the surrogate model with improved expectations is combined to carry out the aerodynamic shape optimization of hypersonic vehicles. The hypersonic aerodynamic optimization design of NACA 0012 airfoil is conducted, which verifies the high efficiency of the optimization method. The single-point and multi-point aerodynamic optimization designs for the Hypersonic Technology Vehicle-2 (HTV-2) type are conducted. The correlation analysis to the fundamental modes of control sections and lift-to-drag ratio is performed, which verifies the accuracy of the design. Completed the single-point and multi-point optimized design of the entire vehicle considering 48 design variables and geometry restrictions with volume not less than 95% of the baseline. The single-point optimization increases the lift-to-drag ratio by 10.91%, and the multi-point optimization ensures that the aerodynamic performance is improved at all flight conditions and reduces the drag coefficient by 4.1% at the large angle of attack condition. The vehicle shape change rule that is controlled by the positively correlated and negatively correlated fundamental modes for the three control sections coincides with the optimized trend. The study demonstrated the effectiveness and practicality of the framework in the aerodynamic design of hypersonic vehicles.