To explore the effects of crop rotation and continuous cropping on the microbial community in tobacco-planting soil at different stages and to clarify whether continuous cropping-induced microbial community imbalance can be alleviated by precise fertilization, providing a basis for improving tobacco yields and mitigating diseases. An experiment was set up in Wangqing County, Jilin Province, with two treatments: 1-year maize-tobacco rotation (R) and 2-year tobacco continuous cropping (C). Soil samples were collected at the cluster, peak, and maturity stages. Soil nutrients were measured and high-throughput sequencing was used to analyze the rhizosphere microbial community structure. Proteobacteria and Acidobacteria were dominant in the cluster stage. Continuous-cropping soil had a higher C. viruginosa abundance, and its microbial community was mainly driven by pH, whereas crop-rotation soil was affected by nutrients. During the peak period, the rotation soil had a higher abundance of actinomycetes and fibrinobacteria. At maturity, the rotation soil had higher actinomycetes and floatycomycetes abundances. Crop rotation increased Acidobacteria and decreased Bacteroidetes. Continuous cropping and crop rotation significantly affected the soil microbial community structure in tobaccoplanting rhizosphere soils. The differences in the distribution of different bacteria reflect their adaptability to soil nutrients and pH, providing a scientific basis for optimizing tobacco planting patterns.