Noise, Vibration, and Harshness (NVH) attribute is needed to be included in the vehicle structure design since improving the NVH characteristics enhances the ride quality experienced by the occupants. In this regard an efficient method to optimize the structural dynamic response of an automotive body is proposed considering the low-frequency NVH performances and the improvement of an automotive structure under the constraint of NVH behavior is investigated by using Design of Experiments (DOE) method. Design of experiments methodology is used for a screening of the design space and for the generation of approximation models while the thicknesses of plates consisting of a Body-In-Prime (BIP) of an automotive are employed as design variables for optimisation whose objective is to increase the first torsional and bending natural frequencies. Central Composite Design (CCD) for DOE sampling and Response Surface Methodology (RSM) are employed to optimise the dynamic stiffness of an automotive body. Moreover, the effect of selected variables as well as their binary interactions, were modeled and the optimum conditions for rigidity improvement were obtained via the RSM. Furthermore, the validity of the proposed optimisation scheme is verified through CAE analysis. The results indicated that first torsion and bending natural frequency were improved without considerable increase in the body weight.