【Objectives】Rhizosphere microorganisms affect the availability and transformation of soil nutrients, which are closely related to the growth and health of plants. Changes in rhizosphere microorganisms with plantation years of Fructus aurantii were studied for better field F. aurantii management. 【Methods】The rhizosphere soil samples of F. aurantii planted for 4 (Y4), 20 (Y20), and 40 (Y40) years in Chongqing were collected on 2020. The changes in diversity index and community composition structure of bacteria and fungi were analyzed by high-throughput sequencing technology, and the correlation between rhizosphere microbial community composition (bacteria and fungal) and soil properties was explored.【Results】Soil organic matter (SOM), total nitrogen (TN), available N (AN), available phosphorus (AP) and available potassium (AK), except pH, were significantly higher (P < 0.05) in Y40 than those under Y4 and Y20. The Shannon and Pielou indices of fungi were significantly increased with the increase in plantation age (P < 0.05), while those of bacteria had no significant changes. The principal coordinate analysis (PCoA) indicated that the rhizosphere bacterial and fungal community structures under Y40 significantly differed from those under Y4 and Y20. At the phylum level, the dominant bacteria phyla were Proteobacteria, Acidobacteria, Actinobacteria and Gemmatimonadetes, and their total relative abundance accounted for 61.07~87.79%. Also the dominant fungal phyla were Ascomycota and Basidiomycota which accounted for 64.70-85.75%. At the genus level, the abundance of beneficial bacteria and fungi in rhizosphere soil under Y40 was significantly lower than those under Y4 (P < 0.05). For example, the abundance of Sphingomonas, Ochrobactrum, Nocardioides, Pseudomonas, Trichosporon and Chaetomium were decreased by 51.21%, 91.32%, 78.60%, 81.87%, 70.58% and 60.74%, respectively. Furthermore, the abundance of pathogenic genera including Fusarium, Plectosphaerella and Ilyonectria, were significantly increased by 117.6%, 323.9% and 1631% under Y40 compared to Y4 (P < 0.05), respectively. The mantel analysis showed that soil pH and nutrient availability were the important abiotic factors influencing the composition of bacterial and fungal communities under different F. Aurantii planation years. 【Conclusions】 Long-term plantation of F. Aurantii altered soil bacterial and fungal community structures. Specifically, the fungal diversity index and the abundance of pathogenic fungi increased, while the abundance of beneficial microbes in the rhizosphere soil decreased. These alterations were the main reasons for inducing an aggravation of the related disease and then a worse plant growth with the increasing age of F. Aurantii plantation.