Background Gastrodia elata is a widely distributed achlorophyllous orchid and is highly valued as both medicine and food. Gastrodia elata produces dust-like seeds and relies on mycorrhizal fungi for its germination and growth. In its life cycle, G. elata is considered to switch from a specific single-fungus relationship ( Mycena ) to another single-fungus relationship ( Armillaria ). However, no studies have investigated the changes in the plant-fungus relationship during the growth of G. elata in the wild. In this study, high-throughput sequencing was used to characterize the fungal community of tubers in different growth phases as well as the soils surrounding G. elata . Results The predominant fungi were Basidiomycota (60.44%) and Ascomycota (26.40%), which exhibited changes in abundance and diversity with the growth phases of G. elata . Diverse basidiomycetes in protocorms (phase P) were Hyphodontia , Sistotrema , Tricholoma , Mingxiaea , Russula , and Mycena , but the community changed from a large proportion of Resinicium bicolor (40%) in rice-like tubers (phase M) to an unidentified Agaricales operational taxonomic unit 1(OTU1,98.45%) in propagation vegetation tubers (phase B). The soil fungi primarily included Simocybe , Psathyrella , Conocybe , and Subulicystidium . Three Mycena OTUs obtained in this study were differentially distributed among the growth phases of G. elata , accounting for less than 1.0% of the total reads, and were phylogenetically close to Mycena epipterygia and M. alexandri . Conclusions Our data indicated that G. elata interacts with a broad range of fungi beyond the Mycena genus. These fungi changed with the growth phases of G. elata . In addition, these data suggested that the development of the fungal community during the growth of G. elata was more complex than previously assumed and that at least two different fungi could be involved in development before the arrival of Armillaria . Electronic supplementary material The online version of this article (10.1186/s12866-019-1501-z) contains supplementary material, which is available to authorized users.