The body freedom flutter frequency is low，and the modal frequency participating in flutter is very close in the subcritical state. In addition，the signal-to-noise ratio of the flutter flight test data based on the atmospheric turbulence excitation is usually low，increasing the difficulty of mode identification and flutter prediction. Therefore，a method of body freedom flutter prediction based on the Matrix Pencil modal identification method is proposed in this paper. The random decrement technique is used to average the output response signals to obtain the random attenuation marks. The Matrix Pencil method is applied to fit the random attenuation marks to attain the modal parameters，and the real modes are then filtered by the frequency and damping stability criteria. The flutter critical points are extrapolated by the damping ratio and flutter stability parameters. Through the application of simulation data and experimental data，the following conclusions could be drawn：the Matrix Pencil modal identification method could effectively identify dense flutter modes，and obtain clear mode identification steady-state diagram. The results of flutter prediction based on the extrapolation of damping ratio and stability parameters are reasonable. The decreasing trend of DTFM（Discrete-Time Flutter Margin）variable is more obvious，and the extrapolation result is closer to the test value. This method is suitable for the subcritical prediction of the body freedom flutter flight test.