<p>Exploring the ecological responses of organisms to environmental heterogeneity reveals crucial insights into environmental filtering processes and species distribution patterns, providing a scientific foundation for wetland management and conservation efforts. Macrobenthos play a major role in wetland ecosystem, yet simultaneously, research on biodiversity patterns and their responses to ecological factors remains insufficiently comprehensive. Therefore, we systematically investigated the spatial structure patterns and driving factors of macrobenthic communities in the Yellow River tidal zone (HT) and the Dawenliu tidal zone (DT) of the Yellow River Delta (YRD) wetland using β-diversity analysis, co-occurrence network analysis, and stability analysis. Our findings demonstrate significant differences in community composition and diversity between HT and DT. The HT exhibits higher species richness, dominated by mollusks (51%) and annelids (45%), primarily explained by salinity variations. Conversely, the DT was dominated by arthropods (74%), influenced mainly by sediment sand content. Our findings indicate that environmental heterogeneity intensifies the role of environmental filtering on species distribution. Species turnover dominated biodiversity changes in HT (52%) and DT (80%), driven significantly by sediment properties. Moreover, our research found that high species nestedness enhances the complexity of co-occurrence networks, thereby strengthening the stability of macrobenthic communities. Our study highlights the significance of species coexistence mechanisms in shaping biodiversity patterns. These research findings enhance our understanding of how environmental heterogeneity regulates community composition and sustains biodiversity, underscoring the necessity for diverse conservation strategies.</p>