In consideration of the affects of rainfall on the radar wave propagation and wave parameter inversion in the sea cluter remote sensing by a radar, a new method combined quality control with the three-dimensional evaluation parameters of surface roughness and signal-to-noise ratio(SNR) is proposed to identify and deal with the rain data to improve the parameter accuracy. Firstly, it analyses the influence of the rainfall on the radar remote sensing and the characteristics of sea clutter,and uses the quality control to identify the data available or not. Then, according to the change trend of the three-dimensional evaluation parameters of surface roughness of radar images and SNR, the reasons that radar images are unavailable are determined and those images affected by the rainfall are identified. Finally, those images which are not seriously affected by rain are chosen to be filtered in frequency domain, and the inversion results with and without filtering are compared with the references.Experiment results show that the relative error of wave period has improved by 19.13%, and the measurement error of wave direction has decreased by 10.54 °. This method can distinguish the rain and non-rain data, and can deal with rain data effectively to improve the accuracy of inversion results.