Debaryomyces hansenii has the potential to enhance the flavor profile of traditional fermented meat products. This study investigates the impact of the D. hansenii LY090 strain on the microbial community, lipidome, flavor profiles, and sensory properties of Sichuan bacon. Inoculation with LY090 significantly inhibited the relative abundance of other yeasts, except for Debaryomyces, and altered bacterial community composition. The presence of LY090 led to a notable reduction (p < 0.05) in the levels of ceramide and phosphatidylcholine, resulting in an excessive inhibition of lipid degradation. This further affected the development of flavor and color in Sichuan bacon. However, the concentrations of aldehydes (249.80 μg/kg), ethyl 3-methylbutyrate (81.01 μg/kg), and acetoin (223.91 μg/kg) were all found to be abundant, and the bacon achieved the highest overall acceptance scores when inoculated with both LY090 and commercial starter culture FAST301. Correlation analysis indicated that the differential metabolites exhibited a stronger association with the yeast community, which plays a vital role in the flavor development of Sichuan bacon. These detailed investigations provide meaningful implications for D. hansenii LY090 implementation strategies in the Sichuan bacon industry.