The invention relates to a building method and application of an Argopecten irradians irradians and Argopecten purpuratus hybrid scallop maintainer line. The maintainer line allows the corresponding male sterility line offspring of the corresponding Argopecten irradians irradians and Argopecten purpuratus hybrid scallop to have male sterile and egg fertile features. The Argopecten irradians irradians and Argopecten purpuratus hybrid scallop is the hybrid offspring of the eggs of the Argopecten irradians irradians and the sperms of the Argopecten purpuratus. The method includes: building a large amount of Argopecten irradians irradians and Argopecten purpuratus hybrid scallop first filial generation families, and finding male sterile individuals, for male sterility line breeding, in the families; using the sperms of male parent Argopecten purpuratus for continuous back crossing, and respectively breeding a male sterility line-maintainer line combination with all the offspring being male sterile individuals; using the male sterility line to hybridize with the retainer line to produce male sterility line parent scallops, and using the male sterility line parent scallop produce Argopecten irradians irradians and Argopecten purpuratus hybrid scallop commercial fry. The method has the advantages that the scallop retainer line is built in animals for the first time, and the barrier of self-fertilization of the hermaphrodite scallops during hybridization is overcome effectively.