A seed selection method of a high stigma exsertion rate japonica two-line sterile line belongs to the fields of two-line hybrid japonica rice genetic breeding and seed production. The method comprises the following steps: 1 choosing a two-line sterile line with a high stigma exsertion rate as a donor parent; 2, hybridizing the donor parent with a japonica two-line sterile line; 3, selecting individual plants with the stigma exsertion rate reaching above 95% from the above obtained F2 generation; 4, selecting materials with high stigma exsertion rate and stable and consistent group properties from the above obtained F3 to F7 generations; 5, carrying out high stigma exsertion rate gene positioning on the obtained materials, and selecting low initial temperature materials by using a greenhouse; 6, hybridizing the materials obtained in step 5 with conventional japonica rice, backcrossing the F2, selecting thoroughly abortive individual plants from BC1F2, cutting spikes, and collecting seeds; 7, continuously inbreeding the obtained materials in Hainan to F4, experimentally planting the BC1F5 in different latitude regions, selecting temperature and light-insensitive sterile individual plants, cutting spikes, and collecting seeds; and 8, carrying out stigma exsertion gene detection on the obtained materials, and finally screening a two-line sterile line material with a high stigma exsertion rate. The method can significantly improve the breeding efficiency and the seed yield.