Nature fermented dry-cured hams may be contaminated by ochratoxin A (OTA) due to the colonization of OTA-producing fungi. Yeast plays essential roles in the formation of the special flavor of ham as well as the potential to retard OTA biosynthesis. In this study, the yeast diversity of Panxian hams fermented from 1 year to 2 years was investigated, revealing a total of 9 yeast genera. The dominant genus switched from Debaryomyces hansenii to Yamadazyma triangularis, while the yeast diversity increased with the prolongation of the fermentation period. Notably, Yarrawia lipolitica GZPX-3Y-1 was identified as a biocontrol yeast strain that can effectively inhibit the OTA biosynthesis up to 82% in OTA-producing modeling media and 55% in ham media when cocultivated with a previously identified OTA producing fungi from Panxian ham, specifically Aspergillus niger A-8. The double-plate methods experiment unveiled that Y. lipolitica GZPX-3Y-1 can only inhibit the growth of A. niger A-8 under the anoxic conditions. Characteristics of Y. lipolitica GZPX-3Y-1 were explored, showing its ability to grow at wide range of temperature (18–33 ℃) and pH levels (pH 3–12). Additionally, it exhibited tolerance to high salt conditions (8%) and demonstrated lipolysis ability without hemolytic ability. These findings indicate the great potential of Y. lipolitica GZPX-3Y-1 to be applied in the fermentation of Panxian ham as a biocontrol strain.