In this study, we tested the feces of children with ASD and those of healthy children, and the overall changing of the community was observed in ASD children compared with controls. However, there were no abundant fungi populations showed significant variations between the ASD and Control group both at phylum and class level. Among the 507 genera identified, "Saccharomyces" and "Aspergillus" showed significant differences between ASD (59.07%) and Control (40.36%), indicating that they may be involved in the abnormal gut fungal community structure of ASD. When analyzed at the species level, a decreased abundance in "Aspergillus versicolor" was observed while "Saccharomyces cerevisiae" was increased in children with ASD relative to controls. Overall, this study characterized the fungal microbiota profile of children with ASD and identified potential diagnostic species closely related to the immune response in ASD.