Surface wave is the main factor that affects signal to noise ratio and resolution in pre-stack seismic data. The traditional methods of suppression of the surface wave have some unavoidable defects. Generalized Stransform can transform the single-channel seismic records from the time domain to the time-frequency domain, make the surface wave and effective wave separated clearly in the time-frequency domain, and cut the surface wave in the time-frequency domain. Removing the surface wave via the generalized S-transform in the pre-stack seismic data is proposed in this paper, the theoretical models and real data results show that this method can remove surface wave while the effective wave also has very good protection, signal to noise ratio and resolution of the data have been greatly improved and avoid spatial aliasing.