Hydrological connectivity is one of the key characteristics that reflect the health and function of estuarine wetland ecosystems, and it has a significant impact on the distribution of estuarine fish communities. This study analyzed the dynamic hydrological connectivity of tidal creeks in the Chongming Dongtan area of the Yangtze River Estuary under different tidal states and its influence on fish community distribution, aiming to provide a scientific basis for the ecological restoration, biodiversity conservation, and water resource management of estuarine wetlands. Twelve hydrological connectivity indicators related to hydrological dynamics and landscape dimensions were selected to explore the relationships and underlying mechanisms between hydrological connectivity patterns and fish distribution patterns. The results showed that factors such as tidal range, the duration of hydrological connection, the duration of flooded retention, the number of nodes, the number of river chains, and the node connection rate β are key hydrological connectivity factors. Canonical correlation analysis (CCA) indicated that the sampling regions within the tidal creek system could be divided into five distinct hydrological connectivity areas, i.e., the high connectivity area during spring tides, the low connectivity area during spring tides, the high connectivity area during neap tides, the low connectivity area during neap tides, and the long-term inundation area. Among them, the high connectivity areas during spring tides, the high connectivity areas during neap tides, and the long-term inundation area are the main habitats of dominant fish species. Dominant fish species exhibited different preferences for different hydrologically connected areas. For example, Xenocypris macrolepis and Pelteobagrus nitidus tended to inhabit the high hydrological connectivity areas during spring tides. Lateolabrax maculatus, Mugilidae, and Gobiidae exhibited a preference for high hydrological connectivity areas during neap tides. Juvenile fish such as Coilia ectenes and Protosalanx chinensis preferred to inhabit areas at the mouths of tidal creeks or near the shore. These findings demonstrate that estuarine tidal creek fish actively exercise selection and exhibit preferences for different hydrologically connected habitats under the influence of tides, which are related to their swimming capabilities, body sizes, and feeding behaviors. This study provides a scientific basis for the ecological restoration of estuarine wetlands and the conservation of fish biodiversity. It also helps to formulate strategies for regulating hydrological connectivity in wetland water resource management, thereby promoting the sustainable development of such ecosystems.