A novel framework is established for accurate modeling of Powered Parafoil Unmanned Aerial Vehicle (PPUAV). The model is developed in the following three steps: obtaining a linear dynamic model, simplifying the model structure, and estimating the model mismatch due to model variance and external disturbance factors. First, a six degree-of-freedom linear model, or the structured model, is obtained through dynamic establishment and linearization. Second, the data correlation analysis is adopted to determine the criterion for proper model complexity and to simplify the structured model. Next, an active model is established, combining the simplified model with the model mismatch estimator. An adapted Kalman filter is utilized for the real-time estimation of states and model mismatch. We finally derive a linear system model while taking into account of model variance and external disturbance. Actual flight tests verify the effectiveness of our active model in different flight scenarios.