The underlying processes affecting community structuring in species composition is of primary importance in community ecology. The relative importance of spatial (dispersal-related) and environmental processes has been a major challenge for understanding the assembly of ecological communities. We examined the relative importance of spatial processes (dispersal-related) and environmental processes (environmental selection-related) in community structure for benthic invertebrates of estuarine wetlands in the Yellow River Delta, China. The benthic invertebrates and environmental factors were sampled and analyzed from 32 sites of estuarine wetlands (19 freshwater restored wetlands and 13 natural wetlands) in October 2017 and May 2018. The results showed that the spatial distribution of benthic invertebrate communities in estuarine wetlands presented obvious differences, and the community structure of benthic invertebrates in freshwater restoration wetlands and natural wetlands was significantly different. The Canonical correspondence analysis (CCA) results showed that the community structure of benthic invertebrates in freshwater recharge area was mainly affected by conductivity (Cond), salinity (SAL), oxidation-reduction potential (ORP) and the influential environmental factor in natural wetlands were pH and inorganic carbon (IC). And there were significant differences among environmental factors, and salinity might be the key factor causing the difference of benthic invertebrate communities' composition between the two types of wetlands. The results of variation partitioning analysis (VPA) showed that environmental factors were more important than spatial variables in regulating benthic invertebrate communities of freshwater restoration wetlands; while in natural wetlands, spatial variables played a major role in regulating benthic invertebrate communities, and the interaction between environmental factors and environmental variables was also crucial in the community. This study clarified the relative effects of environmental and spatial factors on the characteristics of benthic invertebrate communities in the natural and freshwater restored estuarine wetlands, which can provide some reference for biodiversity protection and ecosystem management in estuarine wetlands from the Yellow River Delta.