Soil salinization and alkalization is a key factor limiting the sustainable development of global agriculture. The natural succession of vegetation in saline-alkali soil is an effective method for improving of saline-alkali soil, and microorganisms play an important role in vegetation growth. This study analysed the microbial community structure and diversity of saline-alkali tolerant vegetation rhizosphere soil in northeastern China where natural succession of saline-alkali tolerant vegetation has occurred, using high-throughput sequencing technology. We found that the community structures of bacteria and eukaryotic microorganisms were substantially different with the vegetation natural succession. The bacterial community changed from Actinobacteria-dominated to Proteobacteria-dominated communities. The eukaryotic microorganismal community generally transitioned from alga-dominated (Streptophyta and Ochrophyta) to alga-dominated (Streptophyta and Ochrophyta) and fungi-dominated (Ascomycota) to fungi-dominated (Ascomycota) communities. Based on the difference analysis of microbial community compositions and basic physicochemical properties with the natural succession of vegetation, we found that the bacterial groups that played a key role in the natural succession of the vegetation were Actinobacteria and Proteobacteria and that the eukaryotic microbial groups were Ascomycota, Nematoda, and Streptophyta. The results provide theoretical guidance for microbial inoculation to promote plant succession and improve low-yield saline-alkali soils.