Wild orchids hold significant ecological value, yet current research mainly focuses on germplasm resources, lacking systematic studies on the native habitats and root endophytic fungi of species like Cymbidium goeringii and Cymbidium faberi. This study used fungal sequencing to explore the fungal community in the native habitats of these orchids in the Qinling Mountains. We compared rhizosphere and non-rhizosphere soil fungi and assessed the ecological functions of dominant fungal groups. The impact of soil chemical indicators on fungal communities was also analyzed. Endophytic fungi were isolated from orchid roots to evaluate their growth-promoting potential. Results showed that Ascomycota and Basidiomycota were dominant in the rhizosphere of both species. Symbiotic nutrient and pathology-saprophytic-symbiotic mixed fungal types were predominant, accounting for 56.76% and 79.17% of the fungal community, respectively. Soil factors like total nitrogen and ammonium nitrogen correlated strongly with these communities. A total of 17 fungal strains were isolated, with strains HL01, HL02, HL06, and HL17 exhibiting indole-3-acetic acid (IAA) production, nitrogen fixation, and phosphorus solubilization. Strain HL08 showed IAA production, nitrogen fixation, and potassium solubilization. These strains contribute to enriching growth-promoting fungal resources for both species. This research provides a theoretical and scientific basis for the conservation, artificial cultivation, and breeding of Cymbidium goeringii and Cymbidium faberi.