With the requirements of the speed, maneuverability and agility, the structure with large slenderness ratio is widely employed in the design of the modern rocket. The interaction among unsteady aerodynamic load, structural elastic response, as well as flight motion will be more significant. This paper focuses on the aeroelastic effects in the trajectory simulation of a rotary rocket with a large slenderness ratio. A calculation method based on computational fluid dynamics / computational structural dynamics / computational flight mechanics (CFD/CSD/CFM) coupling system is proposed, in which an in-house CFD/CSD strong-coupled program is connected with the six-degree-of-freedom flight mechanics' equations. The CFD/CSD coupling subsystem as well as CFD/CFM coupling subsystem are validated by aeroelastic dynamic stability analysis of AGARD wing and trajectory simulation of a spinning projectile, respectively. Then, the coupling algorithm is performed on a long-range trajectory simulation of an uncontrolled rotary flexible rocket. The unsteady aerodynamic loads, structural deformation, flight motions, as well as the varying thrust direction are obtained and analyzed. Through the Monte Carlo Experiment, the landing points dispersion of the elastic rocket is also calculated and compared with the rigid case. The results show that the aeroelastic effect can decrease the range and reduce the landing accuracy of the rocket. The proposed method can provide technical support for the correction of the firing table and the design of the control system of the rocket.