Rhizosphere soil microorganisms are critical in the plant's growth and soil health. Continuous crop cropping had significant effects on rhizosphere soil microbial community. To figure out the effects of continuous cropping of Glehnia littoralis on the composition, structure and diversity of rhizosphere soil microbial communities, this study brings to G. littoralis of 1 year (first cropping soil, FS), 2 years (continuous cropping soil, CS), and 0 years (Layland, control soil, CK) soil as the materials. The composition, structure, and diversity of soil fungi and bacteria in different planting years were analyzed by the Illumina high-throughput sequencing technology. The α-diversity of fungi in CS was significantly lower than that in other rotation systems. Proteobacteria, Acidobacteria, and Actinobacteria were the dominant bacteria, and Ascomycota, Basidiomycota, and Zygomycota were dominant phylum fungi. The relative abundance of Actinobacteria and Acidobacteria in the bacterial community decreased with the increase of stubbles, which may significantly reduce the microbial diversity and remedy the negative effects of continuous cropping of G. littoralis. The pH value, urease activity, and total nitrogen content were higher in the continuous cropping soil. Redundancy analysis showed that soil nutrients, pH value, and urease activity had significant effects on soil fungal and bacterial communities. Significant correlations were detected between soil total nitrogen and urease, and between soil total phosphorus and total potassium. In conclusion, continuous cropping changes soil nutrients, pH value, and urease activity, which, in turn, shifts the soil microbial community. The interaction and mutual influence of these factors may be the main cause of continuous cropping obstacle of G. littoralis.