In this study, Debaryomyces hansenii PETY002, isolated from Pu-erh tea, was used for enhanced fermentation (EF) of Pu-erh tea. The total number of yeast colonies was significantly higher in the EF group than in the natural fermentation (NF) group. Sensory evaluation revealed that the tea infusion from the EF group was darker in color, mellower in taste, and had a mushroom-like aroma. Compared with NF, EF showed an increase in the contents of theabrownins and water extracts and a decrease in the contents of tea polyphenols, catechins including catechin (C), epigallocatechin (EGC), gallocatechin (GC) and epigallocahechin-3-gallate (EGCG), and caffeine. On the other hand, there was little difference in the contents of flavonoids or amino acids. Microbial community analysis revealed that Debaryomyces was the dominant fungus in EF. Furthermore, there was a competitive interaction between Debaryomyces and Thermomyces. Correlation analysis revealed that Debaryomyces were positively correlated with theabrownins, but negatively correlated with soluble sugars and theaflavins. In conclusion, inoculation with D. hansenii PETY002 changed the diversity and composition of the microbial community during Pu-erh tea fermentation, which improved the quality of Pu-erh tea through interactions with other dominant microorganisms.