The pen shell, Atrina pectinata, distributes globally. It is one of the most important edible bivalves in east Asian countries. However,there are multiple difficulties in rearing pen shell larvae and juveniles because of their high mortality. To understand the mechanism underlining such high mortality at the early embryonic development stage, we obtained approximately 100 million larvae during later breeding season in June, 2017, and checked a large amount of mitotic chromosomal plates of the early embryos and post-spawning gonads tissue slices of their parents. The results showed that most diploid A. pectinata embryos have 17 pairs of chromosomes ( 2n = 34) as their parents do. The first pair of particularly large chromosomes are heterotypic in some diploid embryos while they are homomorphic in others. The primary sex-determination chromosome type is XX/XY. A lot of triploid, pentaploid and aneuploid embryos with different numbers of the largest homomorphic or heteromorphic chromosomes were found due to the degeneration of overmatured parent gonads which hold normal karyotype. These larvae will die even though most of them may develop into the trochophore stage with 34 chromosomes. Genetic deficiency of chromosomes will cause a high rate of mortality in early embryos in late breeding season. These findings should enrich the current knowledge of juvenile pen shell aquaculture.