The analysis of changes of microbial community in the soil under the rotation of Lysimachia christinae Hance—rice was carried out to provide a theoretical basis for the efficient, high-yield and sustainable cultivation of Lysimachia christinae Hance. High-throughput sequencing technology was used to analyze the composition and diversity of soil microbial communities under the rotation of Lysimachia christinae Hance—rice. The results showed that there was no significant difference in the number of soil bacterial OTU under the rotation of Lysimachia christinae Hance—rice, while the number of soil fungal OUT decreased significantly. The diversity of bacteria, same as fungi, did not change significantly before and after the rotation. The richness of bacteria reduced significantly, but the richness of fungi did not change significantly. At the phylum level, a total of 22 bacterial phyla were detected in the soil including Proteobacteria, Acidobacteria, Actinomycetes, etc., and a total of 8 fungal phyla were detected including Ascomycota, Basidiomycota, and Cystobacteria, etc.. Except that the relative abundance of Acidobacteriaceae increased significantly after rice rotation, the relative abundances of other bacterial phyla and fungal phyla showed a decreasing trend. The Lysimachia christinae Hance—rice rotation could reduce the relative richness of soil microorganisms, especially the relative richness of fungi. The continuous cropping process would make the dynamic succession of soil microorganisms show a trend of increasing the number of fungi. This research could provide a theoretical basis on continuous cropping obstacles and disease reduction under continuous grass planting of Lysimachia christinae Hance.