Microorganisms play an important role in the biogeochemical cycle and ecological function regulation of wetlands. They have a major impact on global climate change and are critical for maintaining the health of the global ecosystem. Taking the coastal wetland of the Yellow River delta as the research object, this study explored the composition of the soil microbial community, rhizosphere microorganisms, environmental factors and their internal correlations and influencing mechanisms by collecting the soil surface layer of representative vegetation communities and part of plant roots. Research results showed that there were differences in microbial diversity among areas with different vegetation covers. The microbial abundance in Phragmites australis and Tamarix chinensis areas was higher than that in mudflat, Suaeda glauca and cotton field. Moreover, the microbial abundance in mudflat was significantly higher than that in washland and floodplain. The structure and diversity of soil flora were significantly higher than those of rhizosphere microorganism: the Shannon index of soil bacteria was about 4-5.5, while that of rhizosphere microorganism was about 0-4. The soil bacteria were mainly Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria, accounting for more than 90% in all samples, while rhizosphere bacteria were mainly Cyanobacteria, Proteobacteria and Actinomycetes, and the differences of flora structure at the genus level were more obvious. The species composition of bacteria in different habitat types and the microbial composition of different sampling sites in the same habitat type were different. The content of environmental factors was related to the habitat type, SO₄^2- and NO₃^- had the highest significance. The content of Mn⁴⁺, Fe³⁺ and hydrolyzed nitrogen in vegetation-covered areas in wetland soil was lower than that in bare mudflats. Redundancy analysis (RDA) showed that pH value had little influence on the bacterial community in wetland soil on a small spatial scale. The explanatory rates of environmental factors at the phylum and genus levels were 89.7% and 86.8%, respectively. K (23.4%), NO₂^- (11.8%), Mn⁴⁺ (9.8%) and Na (8.0%) were the main factors explaining the structural changes and composition of microbial flora at the phylum level. This study provides an ecological perspective for understanding the influence mechanism between wetland microbial diversity and wetland ecosystem function, and help us to understand the distribution and structure of bacteria in the soil and plant rhizosphere of coastal wetlands in the Yellow River delta, which has important guiding significance for the bioremediation of the degraded coastal wetlands in the Yellow River delta.