Abstract: Based on computational fluid dynamics and system identification technique, the reduced order model (ROM) for transonic unsteady aerodynamics stemmed from the structural mode coordinates is firstly established. Coupled aerodynamic state equations, structural state equations and servo state equations, a model for transonic aeroservoelastic analysis are developed. The results computed by analytical method based on ROM are compared with those by CFD direct simulation method, which are used to demonstrate its correctness and precision. The computational efficiency is improved by 1~2 orders while retaining the accuracy of the CFD based direct simulation method. Then the examples show the effect of the sensor’s locations on the aeroservoelastic system. Finally, the study indicates that the addition of structural filter can reduce the effect of the active control system on the open loop aeroelastic system.