In order to understand the spatial distribution and species composition of fish eggs and larvae in Zhongjieshan Islands and their relationship with environmental factors, ichthyoplankton surveys were carried out from May 2010 to February 2012 by using the horizontal and vertical tows. The non-metric multi-dimensional scaling, cluster analysis and canonical correspondence analysis (CCA) were used to analyze the survey data. The results showed that a total of 1783 fish eggs and 67 larvae were collected in two years of horizontal tows, while a total of 576 fish eggs and 59 larvae were collected from vertical tows. In 2010, the dominant species of horizontal tows was Cynoglossus joyneri while the important species of vertical tows were Scorpaeniformes sp. and Auxis thazard. In 2011, the important species of horizontal tows were Cynoglossus joyneri, Leiognathuss sp., Harpodon nehereus, and Engraulis japonicus while the important species of vertical tows were Cynoglossus joyneri, Harpodon nehereus, and Stolephorus chinensis. ANOSIM (analysis of similarity) indicated that there were significant spatial-temporal differences in species composition between the dominant species and important species in fish eggs and larvae. The results suggested that temperature and salinity had great influence on fish eggs and larvae, and summer was an important season for fish spawning. The areas were dominated by small demersal reef fishes, which were important spawning and nursery grounds for demersal fishes such as Sebastiscus marmoratus and Harpodon nehereus.