The invention provides a breeding method of a clam fast growth strain, which is mainly applied to a seed producing strategy of the selective breeding of the hybrid combination of the clams with different geographical colonies. The method comprises the following steps of: hybridizing the Shandong female clam and the Jiangsu male clam to obtain a first filial generation colony which has the advantages of fast growth and good hybridization; taking the individual with fast growth speed in the first filial generation as a basic colony to perform the selective breeding of phenotypic continuous multi-generation; and breeding the clam fast growth strain. The breeding method is simple in operation, is suitable for scale production, improves the growth speed by more than 20% compared with the common produced clam, and has the great significance for improving the yield of the clam production.