The invention belongs to the technical field of japonica hybrid rice seed production, namely, a seed production technology of mixed sowing and mixed harvesting of BT type large-grain three-line nucleo-cytoplasmic interaction sterile lines and restoring lines with restoring genes. Firstly, small-grain varieties with the thousand kernel weight smaller than or equal to 15 g are directionally transformed into small-grain sterile lines or restoring lines with the thousand kernel weight smaller than or equal to 15 g through a traditional manual emasculation cross breeding method; secondly, medium-and-large-grain sterile lines or restoring lines with the thousand kernel weight larger than 25 g are selected to be matched with the small-grain sterile lines or the restoring lines with the thousand kernel weight smaller than or equal to 15 g, it is required that the sowing beginning duration period of the medium-and-large-grain sterile lines or the restoring lines is close to that of the small-grain sterile lines or the restoring lines newly transformed in the first step, and high-advantage combinations are screened from the matched sets; thirdly, when hybrid seeds are produced, male and female parent one-time hybrid direct sowing is performed, or after male parents and female parents are mixed and sown according to a certain proportion, transplantation, or seedling slinging, or mechanical transplanting or mixed harvesting is performed, grains pass a certain-hole-diameter sieve after harvesting, large-grain varieties are left in the sieve, and small-grain varieties pass the sieve.