The East China Sea (ECS) off the Coast of Zhoushan Archipelago, Zhejiang (ECS-CZA) is home to abundant fishery resources and an important spawning, feeding, and nursing ground for a variety of fish species. Due to long-term overfishing, the ichthyoplankton structure has been dramatically altered. Understanding the species composition and distribution of fish eggs and larvae is one of the most essential tasks to accurately regulate fishery resources and formulate effective management policies; however, little is known about the ichthyoplankton in this region. In this study, an integrated strategy of morphology identification (MI) and mitochondrial COI DNA barcoding were used to identify species of fish eggs and larvae collected from the ECS-CZA. MI revealed 15 fish egg species belonging to 12 families and 12 fish larva species belonging to 12 families; in contrast, DNA barcoding altogether identified 30 species, including 18 fish egg species and 13 fish larva species. One species was shared between the egg and larva samples. Our study offers useful tools and critical scientific information for understanding the recruitment, distribution, and conservation management of various fish species in this marine environment.