The invention belongs to the technical field of plant gene engineering and particularly discloses separation and cloning of alleles Sc-j and Sc-i of a pollen fertility gene loca Sc of paddy rice hybrids, and an application in seed breeding. Sc-j encoding of japonica rice and Sc-i encoding of indica rice contain proteins in a DUF1618 structural domain, which are required in normal growth of pollen of paddy rice. The Sc-j only has one gene copy while the Sc-i, in different varieties, has two or three tandem gene copies. In a hybrid between the japonica rice and indica rice, high-level expression products of the Sc-i multi-copy gene can inhibit expression of the Sc-j, which causes hybrid pollen sterility. The invention discloses a hybridization seed breeding method, in which a part of copies of th Sc-i is mutated by utilizing a gene-editing technology, so that the gene dosage effect of the Sc-i is reduced and further fertility of Sc-j pollen in a japonica-indica paddy rice hybrid is recovered, thus overcoming male sterility of a japonica-indica paddy rice hybrid.