Abstract Soil microbial communities are crucial in maintaining the functions of wetland ecosystems. Understanding the microbial community structure and the key factors driving the assemblages of wetland soil microbiota are important to reveal the connections between microorganisms and functions of wetland ecosystems. In this study, soil bacterial community compositions and the factors shaping them were investigated in three groups of wetlands across China, including Tibet plateau wetlands (TW), inland wetlands (IW) and coastal wetlands (CW). Overall, Bacterial community structure and turnover showed distinct patterns in different groups. Bacterial phyla were mainly composed of Proteobacteria followed by Chloroflexi, Acidobacteria, Actinobacteria and Bacteroidetes in all groups of wetland samples. At genus level, random forest model showed that Coprothermobacter and Acetobacter were two most important genera explaining the differences among groups. The abundances of these genera were very low in IW relative to the other two groups. The alpha diversity of IW was significantly higher than those of TW and CW. The relative contribution of environmental factors was larger in the assemblages of bacterial communities in TW and CW than that in IW. The pH and conductivity were recognized as the most important measured environmental factors influencing bacterial community structure. Our results suggested that the bacterial communities of wetlands in different regions were shaped with different mechanisms. The communities in CW and TW regions owned lower alpha diversity and were more influenced by deterministic processes than those in IW. In conclusion, the spatial pattern of soil bacterial community assembly in Chinese wetland was scale-dependent.