The invention discloses an algorithm for automatically extracting a high-wind-speed cloud system region of typhoon based on the data of a microwave scatterometer. The method comprises the following steps: S1, carrying out the meshing processing of the wind speed data and wind direction data, obtained by the microwave scatterometer, of the typhoon region, and forming grid data points; S2, calculating the wind vector of each grid data point; S3, traversing the typhoon region through a window at a set size, obtaining a plurality of window regions, and calculating the wind speed mean value of eachwindow region; S4, taking the window region with the maximum wind speed mean value as a high-wind-speed cloud system region of the typhoon. The method can achieve the automatic extraction of the high-wind-speed cloud system region of the typhoon according to the data of the microwave scatterometer, is short in consumed time, and can meet the requirements of the business development.