Abstract: Coral reef ecosystems are among the most biodiverse marine ecosystems, providing spawning, feeding, and nursery habitats for numerous fish species. Ichthyoplankton, representing the early life stages of fishes, are crucial for fish population recruitment. Their community composition as well as spatial and temporal distribution patterns can effectively reflect fish reproductive recruitment processes and ecological connectivity. However, studies on ichthyoplankton in coral reef islands and reefs of the South China Sea remain limited, and systematic research on the early fishery resources within the Zhubi Reef lagoon is particularly lacking. This knowledge gap has constrained efforts toward the conservation and ecological management of coral reef fishery resources in the South China Sea. This study aimed to investigate the species composition and community structure of ichthyoplankton in the lagoon of Zhubi Reef lagoon in the South China Sea, and to analyze the seasonal variation characteristics of the ichthyoplankton community, providing a scientific basis for the conservation of coral reef fishes. Using samples collected during ichthyoplankton surveys in the spring and autumn of 2018 and 2019 at Zhubi Reef lagoon, species identification was conducted through a combination of DNA barcoding and morphological methods. Community structure characteristics were analyzed using species diversity indices, hierarchical cluster analysis, and non-metric multidimensional scaling (NMDS) ordination. A total of 39 ichthyoplankton taxa were identified, belonging to 9 orders, 23 families, and 27 genera. Among them, 28 taxa were identified to the species level, 7 to the genus level, and 4 to the family level. Perciformes dominated the species composition, accounting for 69.23% of the total, and coral reef-associated species comprised 51.28% of the community. The dominant species of ichthyoplankton varied significantly between spring and autumn over the two years. In the spring of 2018, the dominant species were Scolopsis affinis, Calotomus spinidens, Priacanthus hamrur, and Synodus binotatus. In the autumn of 2018, the two dominant species were C. carolinus and Caesio teres. In the spring of 2019, the four dominant taxa were S. tectus, Ophichthidae sp.1, Macolor niger, and Gymnothorax sp. No dominant species were observed in the autumn of 2019. The Zhubi Reef lagoon exhibits significant seasonal changes in reef fish reproduction, with significant seasonal shifts in larval fish species composition while maintaining overall species diversity. The Zhubi Reef lagoon provides essential spawning and nursery ground for numerous coral reef fishes, as well as for many demersal and pelagic-oceanic fishes. Coral reef fishes in the South China Sea display specific habitat requirements, with low the connectivity of spawning and nursery grounds among different reefs, decreasing further with increasing distance. This study provides crucial data supporting the conservation of fish resources at Zhubi Reef lagoon and fills a knowledge gap regarding early life stages of reef fishes.