In aircraft design, structural optimization and uncertainty quantification concerning transonic aeroelastic issues are computationally impractical, because the iterative process requires great number of aeroelastic analysis. 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 regardless the variation of design variables. 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 900 times higher than traditional ROM method, which demonstrates the feasibility of this method in iterative design process.