In recent years, the relative importance of the processes driving metacommunity composition has aroused extensive attention and become a powerful approach to identify community patterns and their regulatory mechanisms. We investigated variations in the composition of benthic community in restored wetlands and natural wetlands in the Yellow River Delta (Shandong Province, China). First, spatial structures within each wetland were modeled with Moran eigenvector maps. Next, the variation in community structure among local environmental and spatial variables was partitioned using constrained ordination, and the “elements of metacommunity structure” analysis was used to determine the patterns of best fit for species distributions within metacommunities. Finally, the null model was used to analyze non-random patterns of species co-occurrence. The community structure of benthic invertebrates in restored wetlands and natural wetlands differed significantly. The benthic invertebrate metacommunity structure showed a nested distribution in restored wetlands and a quasi-Clementsian structure in natural wetlands. Pure environmental fractions and pure spatial fractions were critical in regulating benthic invertebrate metacommunities of restored wetlands. In natural wetlands, pure spatial fractions and the interaction between environmental and spatial factors (shared fractions) played a major role in the metacommunity. A species co-occurrence analysis showed that species co-occurred more frequently than expected by chance, demonstrating that biotic interactions were not the main driver of metacommunity structures in both wetland types. Accordingly, the benthic invertebrate metacommunity in estuarine wetlands following freshwater releases was mostly determined by environmental and spatial effects, which resulted in a metacommunity with nested distribution. These results are important for biodiversity protection and ecosystem management of estuarine wetlands in the Yellow River Delta.