To investigate the differences and correlations between the chemical composition and root endophytes of two epiphytic methods,including stone epiphytic cultivation(SE) and tree epiphytic cultivation(TE) of Dendrobium nobile in simulated habitat cultivation.Root endophytes were sequenced and analyzed using high-throughput sequencing technology,and preliminarily explored the differences and correlations between chemical composition contents and root endophytes.The results of the study showed that the contents of dendrobine,total alkaloids and total flavonoids were higher in SE than in TE,and the content of total polysaccharides was higher in TE than in SE.The relative abundance of D. nobile root endophyte species differed significantly between the two epiphytic methods,with higher species richness and diversity of D. nobile root endophytes in SE than in TE.Beneficial endophytes increased in SE compared to TE,whereas pathogenic endophytes increased in TE compared to SE.The correlation result revealed that the relative abundance of endophyte genera enriched in SE was significantly positively correlated with dendrobine,however,it was significantly negatively correlated in TE.Meanwhile,the endophyte genera enriched in SE was significantly positively correlated with total flavonoids,total alkaloids and total polysaccharides contents,while the contrary was observed in TE.In conclusion,the elevated chemical compositions in SE compared to TE are related to the fact that SE favors the enrichment of root-endophytic that have plant growth-promoting and nitrogen-fixing effects,which promotes the production of phytochemicals and is conducive to the enhancement of the quality of the herbs.The study lays the foundation for the correlation of "epiphytic methods-root endophyte-secondary metabolites" of D. nobile,as well as the scientific basis for "the Dendrobium grown on the stone has the better quality" of D. nobile.