[Objective] To delineate the fungal diversity characteristics and disparities in the rhizosphere soil of naked barley from fields exhibiting different root rot incidences, thereby informing targeted and effective disease management strategies. [Methods] Rhizosphere soil samples of naked barley were collected from the healthy field and the fields with root rot incidences of 5%, 10%, 15%, and 20%, respectively. The 18S rRNA gene of fungi from the samples was amplified, and high-throughput sequencing was conducted on the Illumina-MiSeq platform. Following quality control, classification, and annotation, the data were analyzed for fungal diversity from various perspectives and taxonomic levels. [Results] The healthy sample and the sample with the root rot incidence of 5% had the highest fungal diversity, while the sample with the incidence of 10% exhibited the lowest diversity. Additionally, co-occurrence network analysis revealed more complex species interactions in the healthy sample and the sample with the incidence of 5%. The root rot incidence had a negative correlation with the relative abundance of Ascomycota but a positive correlation with the relative abundance of Basidiomycota and Glomeromycota. Dominant fungal classes were Agaricomycetes, Chytridiomycetes, and Sordariomycetes. Significant variations in the distribution of fungal groups with high average relative abundance were noted across samples. Specially, the healthy sample had the highest relative abundance of Eurotiales and the lowest relative abundance of Glomerales, which were converse in diseased samples. Arthrodermataceae was significantly enriched in the healthy sample, while Sordariaceae, Myxotrichaceae, and Olpidiaceae were preferentially associated with the samples exhibiting incidences of 10%, 15%, and 20%, respectively. At the genus and species levels, the composition of dominant fungal communities in the healthy sample and the sample with the incidence of 5% was similar, and it was similar in the samples with incidences of 10%, 15%, and 20%. FUNGuild predicted a decrease in the relative abundance of plant pathogens and an increase in the relative abundance of saprotrophs with the increase in disease incidence. [Conclusion] The progression of naked barley root rot is intricately linked to the disruption of the equilibrium within the rhizosphere fungal community. In the context of precision management of naked barley root rot, it is imperative to regulate and sustain the balance of the abundance of dominant fungal taxa in the rhizosphere.