Joint stiffness can affect the vibration characteristics of car body structures. Therefore, it should be included in vehicle system model. In this paper, a numerical approximation of joint stiffness is presented considering joint flexibility of thin walled beam-jointed structures. Using the proposed method, it is possible to optimize joint structures considering the change of section shapes in vehicle structures. The numerical approximation of joint stiffness is derived using the response surface method in terms of beam section properties. The study shows that joint stiffnesses can be effectively determined in designing vehicle structures.