Habitat restoration is a critical measure for conserving fishery resources and maintaining sustainable production. The habitat of juvenile fish in the Yangtze River Estuary has been seriously degraded. In this study, we aimed to identify the effects of tidal flat habitat restoration on fish community structure in the Yangtze River Estuary. Fish samples were collected in the spring, autumn, winter, and summer of 2021–2022 in the south branch of the Yangtze River Estuary. The study was conducted using fixed plug nets in the habitat restoration and control areas. The number of fish species, individuals, biomass, and diversity indices were compared between the restoration and control areas. A total of 27 fish species belonging to 21 genera in 8 orders and 9 families were collected during the study period, of which 22 species were collected in the restoration areas and 21 species in the control areas. The results showed that the total Margalef richness index (D) was 6.8, the total Shannon-Wiener diversity index (H′) was 4.92, the total Simpson simplicity index (C) was 2.47, and the total Pielou evenness index (J′) was 2.99. The overall biodiversity index was significantly higher in the restoration areas (17.18) than in the control areas (15.82). The frequency of fish larvae collected in the restoration areas (67%) was significantly higher than that in the control areas (44%) in the spring, indicating a preference for habitat restoration areas by juvenile fish in the restoration areas. These findings demonstrate that habitat restoration in the tidal flats could alleviate the ecological crisis of fish biodiversity in the Yangtze River Estuary and those restoration areas can provide nursery sites for juvenile fish. This study provides a reference for elucidating habitat restoration in fish nurseries in the tidal flats of the Yangtze River Estuary. In conclusion, enhancing the protection of fish habitats and restoring damaged wetlands is a crucial measure to protect fish resources in the Yangtze River Estuary.