[Background] Gardenia jasminoides Ellis is a perennial evergreen shrub. After years of continuous planting, it will lead to deterioration of the soil micro-ecological environment, aggravation of pests and diseases, and reduced quality. It was found that intercropping was an effective cultivation method in production to improve soil microflora, nutrient and enzyme activity. [Objective] In this study, the dynamic changes of the rhizosphere soil microflora, enzyme activity and nutrients of gardenia under different intercropping patterns were studied, in order to provide a theoretical basis for revealing the soil microecology mechanism of cultivation measures to improve the soil ecological environment and enhance the yield of gardenia.[Methods] To understand the effects of different intercropping patterns on the rhizosphere microecology, three-year-old gardenias were selected for field experiment. Random block design was adopted. Gardenia single cropping and Gardenia/Bletilla striata, Gardenia/Lysimachia christinae, Gardenia/Belamcanda chinensis three intercropping treatment were set, using Gardenia rhizosphere soil as the research material, sampling throughout the growth periods. Illumina high-throughput sequencing technology was used to determine the sequences of bacterial 16S rRNA gene V3—V4 and fungal rDNA ITS1—ITS2, and the physical and chemical properties of the soil in each period were determined, so as to clarify the intercropping of different crops on the gardenia rhizosphere microbial community and soil physical and chemical properties with the growth period.[Results] In the whole growth process of gardenia, the relative abundance of Proteobacteria and Acidobacteria in the rhizosphere bacterial community were 39% and 18%, respectively, which were the dominant bacteria. In the fungal community, the relative abundance of Ascomycota, Basidiomycota and Mortierellomycota accounted for 51%, 22% and 19%, respectively, which were the main fungal groups. In the fruit expansion stage, compared with single cropping, Gardenia/Belamcanda and Gardenia/Bletilla striata can significantly increase the Shannon index of soil bacterial communities by 6.55% and 3.45% (P<0.05), respectively, but there was no significant difference at other stages. In terms of rhizosphere fungi, Gardenia/Belamcanda does not significantly reduce the diversity during the full blooming period, while intercropping with Lysimachia or Bletilla will significantly decrease; In the fruit expansion stage, Gardenia/Belamcanda and Gardenia/Bletilla intercropping can significantly increase the Shannon index of the rhizosphere soil fungal community by 29.19% and 9.12%, respectively. In terms of soil nutrients, The contents of organic matter, total N and available P in rhizosphere soil of gardenia monoculture were higher, while the contents of alkaloid N and available K were lower than the three intercropping treatments. In terms of soil enzymes, except for the acid protease, the activities of the other soil enzymes of the single-cropped gardenia are at a lower level. Correlation analysis between soil physical and chemical properties and rhizosphere microbial diversity showed that the bacterial diversity index Shannon was significantly positive correlated with rhizosphere soil organic matter, available P, and extremely significantly positive correlated with pH (P<0.01); The fungal diversity index Shannon was significantly negative correlated with total K, urease and catalase in rhizosphere soil, and significantly positive correlated with available K, sucrase, acid phosphatase, and acid protease activities. The comprehensive scores of soil fertility in the blooming stage and fruit expansion stage showed that the soil fertility scores of Gardenia/Belamcanda was the highest, and that of Gardenia/Lysimachia was the lowest.[Conclusion] Reasonable intercropping can improve the microbial community structure in the rhizosphere, and improve the comprehensive soil fertility. The soil fertility comprehensive score of Gardenia/Belamcanda is the highest, they may be the desirable intercropping patterns for Gardenia cultivation.