This study identifies four stable fungal enterotypes in the human gut mycobiome, which are closely associated with bacterial enterotypes and significantly correlated with host factors such as age and disease. The Can_type enterotype, dominated by Candida, is enriched in the elderly population and is linked to an increased risk of multiple diseases associated with a compromised intestinal barrier. Bidirectional mediation analysis reveals that the Can_type-associated aerobic respiration pathway mediates the association between aging and a compromised intestinal barrier. The study also shows that the gut mycobiome has stable compositional patterns across individuals and is significantly correlated with multiple host factors, including diseases and age. The findings highlight the clinical relevance of fungal enterotypes and their potential role in host-microbe interactions. The study used ITS sequencing and metagenomics data from 3363 samples across 16 cohorts, including 572 new samples from China. The results demonstrate that fungal enterotypes are influenced by host phenotypes, with age having a significant effect on fungal composition. The Can_type enterotype is associated with higher intestinal aging and disease risk, while other enterotypes are linked to lower disease risk. The study also identifies functional differences across fungal enterotypes, with the Can_type enriched in pathways related to heme biosynthesis and aerobic respiration, which may contribute to disease risk. The findings suggest that fungal enterotypes play a significant role in shaping the gut microbiome and its association with host health. The study highlights the importance of considering both fungal and bacterial communities in future research on gut microbiome aging.This study identifies four stable fungal enterotypes in the human gut mycobiome, which are closely associated with bacterial enterotypes and significantly correlated with host factors such as age and disease. The Can_type enterotype, dominated by Candida, is enriched in the elderly population and is linked to an increased risk of multiple diseases associated with a compromised intestinal barrier. Bidirectional mediation analysis reveals that the Can_type-associated aerobic respiration pathway mediates the association between aging and a compromised intestinal barrier. The study also shows that the gut mycobiome has stable compositional patterns across individuals and is significantly correlated with multiple host factors, including diseases and age. The findings highlight the clinical relevance of fungal enterotypes and their potential role in host-microbe interactions. The study used ITS sequencing and metagenomics data from 3363 samples across 16 cohorts, including 572 new samples from China. The results demonstrate that fungal enterotypes are influenced by host phenotypes, with age having a significant effect on fungal composition. The Can_type enterotype is associated with higher intestinal aging and disease risk, while other enterotypes are linked to lower disease risk. The study also identifies functional differences across fungal enterotypes, with the Can_type enriched in pathways related to heme biosynthesis and aerobic respiration, which may contribute to disease risk. The findings suggest that fungal enterotypes play a significant role in shaping the gut microbiome and its association with host health. The study highlights the importance of considering both fungal and bacterial communities in future research on gut microbiome aging.