In structural design, iterative design processes, such as optimization and uncertainty quantification, are computationally impractical when transonic aeroelastic issues are involved, because aeroelastic analysis should be carried out at each iterative step. Emerging Reduced-Order Model (ROM) method is convenient for transonic aeroelastic analysis. However, current ROMs cannot be reused during iteration, thus time cost is still way too large. This study proposed an improved ROM suitable for Arbitrary Mode Shapes (ROM-AMS), which is reusable in each iterative step. By adopting Principal Component Analysis, ROM-AMS method can significantly reduce the number of basis mode shapes and improve the accuracy of flutter analysis. In an optimization case, the weight of cropped delta wing is reduced by 28.46%, and the efficiency is two orders of magnitude higher than traditional ROM method, which demonstrates the feasibility of this method in iterative design process.