The structure and temporal variations of the fish community in the intertidal estuarine zone of shallow mud areas have been poorly studied in China. This paper analyses the diel, semi-lunar and seasonal patterns of fish assemblages in the Yangtze estuary in 2006. Fish were collected by consecutive day and night samplings using tide-stow-nets deployed parallel to each other in three stations. A total of 56 fish species belonging to 21 families was caught during the study period. The family Cyprinidae dominated with 25 species. Freshwater fish species were the important dominant commercial fishery species and well represented with five species (sharpbelly Hemiculter bleekeri, goldfish Carassius auratus, bream Parabramis pekinensis, likely-bream Pseudobrama simony, and glossy yellow catfish Pelteobagrus nitidus) in the three stations. Juvenile fishes dominated the fish community, comprising 93.9% in station 1 and 96.6% in station 2 of the total abundance. The number of fish species in day tides was slightly lower than those in night tides in spring and summer, but the opposite in other seasons. In neap tides, the numbers and abundance of fish species were both lower than those in the spring tides. Fish abundance was lowest in winter, increasing during spring and summer (March–September) in both stations 1 and 2, with obviously large fluctuations in each season. The pattern of habitat selection of fishes could effectively decrease the food competition of intraspecies or interspecies and favour the growth and nursing of young fishes. These findings indicate that the intertidal zones in the estuary may serve as important nursery areas for fish communities.