[1]¿p#1 Microorganisms play a pivotal role in maintaining ecosystem functions and stability. However, the distribution patterns and underlying drivers of microbial communities remain poorly understood. By sampling along a latitudinal gradient (18.22 °N to 40.61 °N) in sandy intertidal zones of China, we examined the distribution patterns of bacterial and fungal communities. We applied general linear models, variation partitioning, and network analyses to high-throughput sequencing data. Our results revealed that bacterial α-diversity was significantly higher in the southern zone than in the middle and northern zones, primarily driven by mean annual temperature (MAT) and salinity. In contrast, fungal α-diversity showed no significant difference among the three zones and was predominantly influenced by beach index representing the physical conditions and beach width. Network analysis based on positive correlations revealed the lowest bacterial connectivity in the southern zone, likely due to intensified competition under higher MAT and reduced cooperation under stable climate. However, fungal connectivity was significantly higher in the middle zone than in the northern zone, primarily due to the increase in nutrients brought by the injection of fresh water from the Yangtze River, which potentially increased fungal cooperation and altered coexistence patterns. Moreover, bacterial communities exhibited a faster turnover rate than fungal communities with increasing local environmental heterogeneity, indicating that bacterial communities are more influenced by environmental selection. Overall, these findings underscore the distinct distribution patterns and environmental drivers of bacterial and fungal communities, deepening our understanding of predicting microbial community responses and stability in sandy intertidal ecosystems under environmental change.