Island-type coastal wetland constitute a distinct category of wetland ecosystems. Exploring the mechanisms shaping biodiversity patterns is a central issue in island biogeography. In 2023, this study set up 7 monitoring sections in the Jiuduansha shoal in the Yangtze River Estuary, covering Shangsha, Zhongsha, Xiasha and Jiangyansha of the wetland. The structural characteristics and diversity patterns of the macrobenthic communities were investigated in the different seasons and habitats, and the relationship between β-diversity components of Replacement and Nestedness and community structure was further analyzed. The results revealed that: (1) The 34 recorded macrobenthic taxa belonged to 5 phyla and 7 classes, with Arthropoda demonstrating dominance at 42% of total abundance; (2) The mean Shannon-Wiener diversity, evenness, and richness indices were the highest in the middle tidal zone with the Scirpus mariqueter and Zizania latifolia habitats, followed by high tidal zone habitats with Phragmites australis and Spartina alterniflora habitats, and the lowest values were observed in the low tidal zone with bare flats; (3) The species composition of the macrobenthic communities was significantly different among the habitats, with the Replacement ratio of β-diversity being 45.11%-64.53% and the Nestedness ratio being 22.26%-34.14%. This indicates that the spatial difference of diversity mainly resulted from the Replacement effects of species in the communities; (4) The β-diversity and its Replacement components exhibited distance-decay relationships, suggesting dispersal limitation shapes diversity patterns through species turnover. These findings enhance our understanding of biodiversity patterns in island-type coastal wetlands and are helpful for biodiversity conservation in the Jiuduansha Wetland.