[Background] Erigeron breviscapus is a famous Chinese medicinal plant, while little is known about the diversity, community structure, and ecological roles of endophytic fungi (EF) in this plant. [Objective] To reveal the diversity, community structure, and ecological roles of EF in E. breviscapus. [Methods] The high-throughput sequencing of the ITS region was performed to profile the fungal community in the roots, stems, leaves, and flowers of E. breviscapus in Yunnan. FUNGuild was employed to predict the ecological functions of the fungi. [Results] A total of 540 operational taxonomic units (OTUs) were obtained from 12 samples. All of the OTUs were assigned into 188 genera, 114 families, 55 orders, 22 classes of 5 phyla. Only 14.45% of OTUs were shared by the four medicinal parts, and the unique OTUs were the most in the roots. Ascomycota and Basidiomycota were the dominant phyla in all the samples. The EF in the roots and flowers were dominated by Ascomycota and Basidiomycota, respectively. Didymella was the dominant genus, existing in all the four organs. Other dominant genera were Filobasidium, Cystofilobasidium and Plectosphaerella. The dominant and unique genera of EF varied in the four organs of E. breviscapus. The alpha diversity analysis showed that the roots had the highest richness of EF, while there was no significant difference in the diversity of EF among the four organs. Principal coordinate analysis indicated that the EF had similar community structures between leaves and stems, while the composition of EF in roots was different. FUNGuild prediction revealed that saprophytic fungi accounted for a high proportion in the EF of different samples and contained a large number of undefined taxa. [Conclusion] The EF of E. breviscapus has significant differences in community structure among different organs and demonstrates organ specificity. The findings provide a theoretical reference for the further development and utilization of EF resources in E. breviscapus.