The main goal of present paper is to construct an efficient reduced order model (ROM) for aerodynamic system modeling. Proper Orthogonal Decomposition (POD) is presented to address the problem. First, the snapshots are collected to form the POD kernel, and then Singular Values Decomposition (SVD) is used to obtain POD modes, finally POD-ROM can be constructed by projecting full order aerodynamic system to POD modes subspace. However, the robustness of ROM constructed via conventional POD method is not guaranteed. To improve the robustness of conventional POD method, balanced truncation modification was introduced. Aero-elastic active control case was chosen for this new method validation. The results demonstrate POD method with balanced modification is efficient and accurate enough for aeroelastic system analysis.