Abstract: Due to limited vertical resolution, the waveform of vegetation whose height is relatively low will superpose on soil waveform. Therefore, LIDAR full-waveform data is mainly used in forestry, but no research in the crops. In this paper, in order to derive crop height, a gaussian decomposition algorithm based on transmitting waveform was adopted to distinguish the crop waveform from soil waveform, and to extract peak location and pulse width from raw waveform data. The method was proved a reliable and high accurate decomposition algorithm. Moreover, the decomposition algorithm lays the proper foundation for obtaining other crop biophysical parameters.