ObjectiveTo investigate the effects of different cultivation modes on the yield of Gentiana crassicaulis and its microbial diversity and secondary metabolite content in the rhizosphere soil. MethodWith G. crassicaulis of different cultivation modes and its rhizosphere soil as the research objects， the composition of bacterial and fungal communities， dominant bacteria， and differential microorganisms in the rhizosphere soil were analyzed by high-throughput sequencing technology. HPLC was used to determine the content of iridoids in G. crassicaulis with different cultivation modes. ResultCompared with plastic film mulching， planting without mulch and intercropping of peony， white kidney bean， potato， and corn increased the yield of fresh products by 16.11%-17.68%， 22.48%-26.34%， 29.37%-32.19%， 34.82%-36.57%， and 35.34%-39.71%， respectively， and increased the yield of dry products by 19.75%-23.17%， 25.86%-29.32%， 30.18%-34.94%， 35.22%-39.87%， and 39.72%-43.73%. The total content of four iridoids， including gentiopicrin， loganic acid， sweroside， and swertiamarin， increased by 10.17%-37.83%， 5.93%-47.44%， 9.09%-28.84%， and 10.71%-28.57%， respectively. The diversity of bacterial and fungal communities in the rhizosphere soil increased significantly （P<0.05）. The relative abundance of pathogenic bacteria such as Sordariomycetes， Leotiomycetes， Tremellomycetes， Eurotiomycetes， Fusarium， and Cladophialophora decreased， and the proportions of beneficial bacteria such as Proteobacteria， Acidobacteria， and Actinobacteriota increased and they gradually became the dominant bacteria. ConclusionDifferent cultivation modes can affect the yield of G. crassicaulis and its microbial diversity and iridoid content in the rhizosphere soil. Cultivation without mulch and intercropping patterns have certain advantages， which can provide theoretical references for the planting of G. crassicaulis.