Abstract: The ecological freshwater replenishment project in the Yellow River Delta has exerted a substantial influence on the distribution pattern of biodiversity. To investigate the response of the macrobenthic community structure to this water recharge initiative, during the spring and summer in 2018 and the summer in 2019, macrobenthic samples were collected from the restoration wetland under freshwater replenishment and the natural tidal wetland within the Yellow River Delta. Subsequently, correlation and clustering analyses were conducted. The results revealed that a total of 86 macrobenthic species, belonging to 4 phyla and 8 classes, were documented. Freshwater replenishment induced spatial variations in the macrobenthic community structure. In the restoration area, aquatic insects were preponderant, with a higher species number compared to the tidal area. However, the annual average abundance and biomass were lower than those in the tidal area. Moreover, freshwater replenishment diminished the structural similarity of the macrobenthic communities between the restoration and tidal areas. The species-composition matrix exhibited a significant negative correlation in both spatial and temporal dimensions, which might be associated with species breeding patterns and the effects of water recharge on salinity, vegetation, and species immigration. Comparison with historical data demonstrated that the macrobenthic community in the restoration wetland inclined towards freshwater species. The dominant species displayed miniaturization characteristics, the Shannon-Wiener diversity index fluctuated, and the biomass was considerably lower than that in the tidal wetlands. The findings of this study offer a reference for the adjustment of the ecological water recharge project in the Yellow River Delta and the conservation and restoration of wetland biodiversity, including macrobenthos.