The bay scallop (Argopecten irradians irradians) is one of the most important shellfish species in China. Since their introduction into China, only mass selection has been used in bay scallop breeding. With its gradual expansion and shortage of mate selection, population homozygosity increased, and fitness decreased. To investigate the effects of inbreeding and provide reference for improving breeding strategies and mating management, the variance components of the growth traits of the bay scallop were decomposed with genomic relationship matrices. The results indicated that the genetic variations in shell height and length were mainly accounted for by the additive effects. The genetic variation in shell width was mainly caused by dominance or dominance-by-dominance epistasis. The genetic variation in body weight was accounted for by dominance. No significant directional dominances were detected for all growth traits. Cross-validation for genomic prediction showed that including insignificant inbreeding in the genomic prediction model is not necessary, and we suggest that the genomic prediction model should be optimized with both likelihood ratio tests and cross-validation before utilization in practice.