Aerodynamic and aerothermal prediction are critical and fundamental to hypersonic vehicle design. Traditional engineering methods are no longer applicable in assembly configuration of real vehicles, while high-precision computational fluid dynamic (CFD) method is too costly to support significant computational requirement in multi-case analysis. In this paper, the aerodynamic load characteristics of the rudder attached to a hypersonic missile body are investigated, including the aerodynamic pressure and aerodynamic heat flow. First, the results of an independent rudder and the assembly are calculated and compared. The calculation process involves the third-order piston theory, the Eckert reference temperature method, and CFD. Then, this study proposes and discusses a medium-fidelity analysis method that uses limited CFD result data to modify the engineering methods. The findings indicate that the missile body exerts an influence on near-wall flow pattern of the rudder, thereby amplifying the three-dimensional flow effect of the rudder. It also demonstrates that it is possible to capture these effects with adequate computational efficiency through the modified method provided in this paper. The modifying effect for integral heat flow is significant, eliminating almost all disparities. While that for integral force is obvious for some angles-of-attack conditions in this paper, reducing integration disparities compared with the CFD results by about 10%. It is expected that the method presented in this paper may promote a more profound application of engineering methods in hypersonic industry.