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. Two problems are addressed: (1) aerodynamic data inverse design; (2) aeroelastic structure active control. For the second problem, POD method with balanced modification is introduced to improve the robustness of original POD method. Results in problem (1) suggest POD method works efficiently not only for interpolation inverse design but also for extrapolation problems. The results in problem (2) demonstrate POD method with balanced modification is efficient and accurate enough for aeroelastic system analysis.