Significant wave height(SWH) is one of the important parameters which describe the sea state. The SWH derived from altimeter has been widely applied in marine research. Based on HY-2 altimeter waveform data, we develop an inversion algorithm of SWH with high-resolution. Using the RMSE condition to improve the accuracy 20 Hz SWH. Applied this method to one pass waveform data, the result shows the inversion algorithm is effective. Comparing the SWH derived from 1 s waveform, the SWH derived by this method could be increased by about 15 times the spatial and temporal resolution observations and the accuracy is about 0.44 m. The SWH derived from HY-2 altimeter 20 Hz waveform is reliable and could be applied for high resolution marine research.