Aerodynamic force can lead to the strong structural vibration of flying aircraft at a high speed. This harmful vibration can bring damage or failure to the electronic equipment fixed in aircraft. It is necessary to predict the structural dynamic response in the design course. This paper presents a new numerical algorithm and scheme to solve the structural dynamics responses when considering fluid–structure interaction(FSI). Numerical simulation for a free-flying structural model in transonic speed is completed. Results show that the small elastic deformation of the structure can greatly affect the FSI. The FSI vibration tests are carried out in a transonic speed windtunnel for checking numerical theory and algorithms, and the wind-tunnel test results well accord with that of the numerical simulation. This indicates that the presented numerical method can be applied to predicting the structural dynamics responses when containing the FSI.