High-throughput sequencing was conducted on Erigeron breviscapus rhizosphere soil over one, two, and three years to analyze continuous cropping effects on the microbial community structure. There was a decrease in yield and the soil properties changed. Soil ammonium nitrogen and total phosphorus content increased annually, while soil hydrolyzed nitrogen and available phosphorus content decreased annually. Compared with that of the CK, soil total potassium, available potassium, and nitrate nitrogen content and cation exchange capacity all increased, which showed a decreasing trend followed by an increase in planting years. Nine bacterial phyla, with Proteobacteria, Firmicutes, Acidobacteria, Actinomycetes, Blastomonas, and Bacteroidetes as the dominant phyla. Among them, the Proteobacteria phylum highest relative abundance was significantly and positively correlated with total nitrogen (TN) and quick potassium content (P＜0.05) , and cation exchange. Five fungal phyla were detected, namely Ascomycetes, Mortierellomycota, Potentillomycetes, Rhodophyta, and Stramonium.