The invention provides a high-yield crossbreeding method of two-line super rice parent GuiKe-2S stock seeds. The high-yield crossbreeding method comprises the following steps: A, carrying out phenotypic screening on a GuiKe-2S large group, namely, planting a GuiKe-2S group of a single plant; B, detecting a specificity marker of a GuiKe-2S sterile locus; C, detecting a molecular marker of a GuiKe-2S fingerprint spectrum; D, carrying out low-temperature screening on a GuiKe-2S first-time manual climatic box; E, carrying out low-temperature screening on a GuiKe-2S second-time manual climatic box; and F, breeding a rice root in winter of Hainan, transplanting the GuiKe-2S the root of which is cut again to Sanya of Hainan for breeding in winter, and harvesting seeds when ripening to obtain the two-line super rice parent GuiKe-2S stock seeds. According to the high-yield crossbreeding method, the stock seeds are further bred to obtain high-purity parent seeds applied to seed production, which has a very important significance in developing two-line hybrid rice. Through tests, the purity of the obtained breeder seeds reaches above 99.99 percent, and the purity of the stock seeds obtained through expanding propagation reaches above 99.9 percent.