Data acquired in December 2004 by GeoChirpⅡsubbottom profiler in the South Channel of the Changjiang Estuary displays maximum amplitude round the seafloor and small signalnoise ratio of the acoustic record. In terms of the features of acoustic record reflected by the seafloor, the sampling area including the seabed is determined in the figure of the profile. Then the method of amplitude is adopted to implement the recognition of the seabed reflection signal and the automatic pickup of seabed topography. Finally, the seafloor picked up is smoothed. The method mentioned above was used to process the data acquired from the South Channel of the Changjiang Estuary. Compared with the original seabed topography, the seafloor picked up automatically demonstrates the rhythm of undulate seafloor, indicating that this method is effective in the recognition of the seabed reflection signal and the automatic pickup of seabed topography.