Wind measurement using spaceborne scatterometers has been used for various scientific and operational purposes. However, the major problem of such measurements is contamination by rain. To improve the wind measurement using the HY-2A scatterometer under rainy conditions, a neural network-based model was established in this study. The model is almost autonomous in that it only needs the backscatter coefficient measurement data and the observation geometry information from the HY-2A scatterometer itself. The model can distinguish between rain-contaminated wind pixels and rain-free wind pixels and significantly improve the accuracy of wind speed measurements using HY-2A scatterometer alone. TAO data and linearly calibrated ECMWF data were used in the study to validate the neural network-inverted wind speed. Under no rain conditions, the RMS of the neural network-inverted wind speed and TAO wind speed was 1.06 m/s, with a deviation of −0.21 m/s, which is a small difference from the standard method inverted wind speed. Under rain conditions, the RMS and deviation were 1.94 m/s and 0.66 m/s, respectively, which were better than the statistical results of the conventional maximum likelihood estimation method. The validated results using linearly calibrated data also indicate that the neural network-inverted wind speed is closer to the validation data under rain conditions.