Continuous cropping can often deteriorate soil quality and reduce crop yield. Soil properties and microbial communities usually play a vital role in maintaining rhizosphere micro-ecosystem sustainability, which is yet to be addressed in continuous peony monoculture systems. Herein, variations in soil physiochemical properties were extensively investigated following 1, 4, and 10 years of continuous tree peony cropping, as well as microbial community diversity, composition, and predicted functions. The soil pH and contents of available Mg, Mn, Zn, and B significantly declined after 10 years of continuous monoculture, while the contents of soil organic carbon, nitrate, and available P, K, Fe, and Cu notably increased by more than 100%, implying an imbalance of soil nutrients resulting from long-term continuous cropping. High-throughput sequencing results indicated that the microbial community structure and composition were remarkably altered after either 4 or 10 years of continuous cropping, interfering with diverse microbial metabolic pathways and phenotype functions. In addition, the relative abundances of some beneficial bacteria dramatically increased, especially for Acidobacteriota and Bacillus members. Microbial selections or adaptations in response to soil nutrient changes were expected to remediate negative impacts of continuous cropping on soil quality. Findings in this study provide insights into the establishment of proper management strategies for sustaining soil quality to resist potential obstacles after long-term continuous peony cropping.