Fish composition and diversity in the Oujiang estuary was studied here based on the data from two oceanographic surveys in June and September of 2007. The spatial-temporal distribution of fish richness and diversity (H′), which was influenced by factors such as topography and geomorphy, water masses, and hydrological features, was also discussed here. Results showed that among 64 species that were identified,16 species were temperate warm water species, and the rest 48 species were warm water species. Pennahia argentatus was the key species in June, and Harpodon nehereus was the key species in September. More species inhabited in the water passage between islands than in other waters. The distribution pattern of diversity (H′) showed that high values lay in the water passages around islands. On the other hand, the diversity (H′) in the east area was clearly lower than that in the west, which was due to the diversified marine topography, geomorphy, deposit and hydrological factors near the islands. The dominant species, Pennahia argentatus in June and Harpodon nehereus in September, mostly distributed in the outer area of islands, was the main reason for the low fish diversity (H′) there. Low richness was the subordinate factor. Seasonal and regional Oujiang freshwater and Taiwan current were critical factors that affected the fish diversity in this area. The species richness was higher in September than that in June because some species migrate to wintering ground in offshore waters off the estuary.