Abstract: Many aerodynamic applications require the modeling of compressible flows in or around a body, e.g., the design of aircraft, inlet or exhaust duct, wind turbines, or tall buildings. Traditional methods use wind tunnel experiments and computational fluid dynamics (CFD) to investigate the spatial and temporal distribution of the flows. Although they provide a great deal of insight into the essential characteristics of the flow field, they are not suitable for control analysis and design due to the high physical/computational cost. Many model reduction methods have been studied to reduce the complexity of the flow model. There are two main approaches: linearization based input/output modeling and proper orthogonal decomposition (POD) based model reduction. The former captures mostly the local behavior near a steady state, which is suitable to model laminar flow dynamics. The latter obtains a reduced order model by projecting the governing equation onto an \"optimal\" subspace and is able to model complex nonlinear flow phenomena. In this research we investigate various model reduction approaches and compare them in flow modeling and control design. We propose an integrated model-based control methodology and apply it to the reduced order modeling and active flow control of compressible flows within a very aggressive (length to exit diameter ratio, L/D, of 1.5) inlet duct and its upstream contraction section. The approach systematically applies reduced order modeling, estimator design, sensor placement and control design to improve the aerodynamic performance. The main contribution of this work is the development of a hybrid model reduction approach that attempts to combine the best features of input/output model identification and POD method. We first identify a linear input/output model by using a subspace algorithm. We next project the difference between CFD response and the identified model response onto a set of POD basis. This trajectory is fit to a nonlinear dynamical model to augment the linear input/output model. Thus, the full system is decomposed into a dominant linear subsystem and a low order nonlinear subsystem. The hybrid model is then used for control design and compared with other modeling methods in CFD simulations. Numerical results indicate that the hybrid model accurately predicts the nonlinear behavior of the flow for a 2D diffuser contraction section model. It also performs best in terms of feedback control design and learning control. Since some outputs of interest (e.g., the AIP pressure recovery) are not observable during normal operations, static and dynamic estimators are designed to recreate the information from available sensor measurements. The latter also provides a state estimation for feedback controller. Based on the reduced order models and estimators, different controllers are designed to improve the aerodynamic performance of the contraction section and inlet duct. The integrated control methodology is evaluated with CFD simulations. Numerical results demonstrate the feasibility and efficacy of the active flow control based on reduced order models. Our reduced order models not only generate a good approximation of the nonlinear flow dynamics over a wide input range, but also help to design controllers that significantly improve the flow response. The tools developed for model reduction, estimator and control design can also be applied to wind tunnel experiment.