An efficient method for transonic aeroservoelasticity based on computational fluid dynamics (CFD) is presented. By using system identification technique, CFD based reduced order model (ROM) for transonic unsteady aerodynamics is constructed. Coupling aerodynamic state equations, structural state equations and servo state equations, a model for transonic aeroservoelastic analysis is built. The examples show the aeroservoelastic characteristics of a typical missile in transonic flow. The results of the open loop problem are compared with those by CFD direct simulation method showing the correctness and quality of the ROM based analysis method. The effects of the sensor position and the addition of structural filter on the aeroservoelastic system of a transonic missile are studied.