Fungi remain understudied in the human gut owing to marker-specific analytical challenges and fragmented datasets. Here, we developed MycoGAP, a gut-focused, ITS-aware workflow for standardized reanalysis of heterogeneous datasets. Using MycoGAP, we constructed the Human Gut Mycobiome Atlas from 46,400 samples spanning diverse populations and linked to harmonized metadata, yielding 3.1 billion microfungal sequences. Together, MycoGAP and the Atlas provide a standardized framework and global resource for understanding gut fungal ecology and its relevance to human health.