Mangrove sediments harbor complex bacterial communities that play critical roles in ecosystem functioning. In this study, we investigated the spatial patterns and environmental drivers of sediment bacterial communities across intertidal flats and vegetated zones in five representative mangrove habitats spanning the Northern Beibu Gulf, South China. Utilizing high-throughput 16S rRNA gene amplicon sequencing, we analyzed bacterial composition and diversity from sediments collected in Qinzhou, Fangchenggang, and Beihai. Results indicated that bacterial communities were dominated by Proteobacteria (37–45%), followed by Bacteroidota and Acidobacteriota; however, a considerable proportion of taxa remained unclassified, particularly in intertidal flats. Bacterial richness and diversity were generally higher in vegetated zones, where sediments were more acidic and nutrient-rich, whereas intertidal sediments were more alkaline and contained higher chlorophyll-a (Chl-a) concentrations. Beta-diversity analysis revealed distinct differences in community structures between zones and regions, which were shaped by both deterministic environmental filtering and stochastic processes. Redundancy analysis (RDA) indicated that bacterial communities assembly driven by niche differentiation influences salinity (Sal), pH, biogenic silica (BSi), total phosphorus (TP), and total nitrogen (TN), as these factors vary across sites due to differing environmental filtering intensities. These findings highlight the distinct differences in mangrove sediment bacterial communities between intertidal flats and vegetated zones, which are shaped by local sediment physicochemical conditions and regional environmental gradients. They provide critical insights for the conservation and restoration of mangrove ecosystems.