Abstract: In order to solve the problem of the thin flavor of Yunnan sweet rice wine. This study had focused on locally screened high alcohol producing Saccharomyces cerevisiae LF05 and high esters producing Rhodotorula mucilaginosa PL10, investigating the effects of their mono- and co-fermentation with Rhizopus oryzae on the physicochemical properties, sensory characteristics, free amino acids, and volatile compounds of the wine. The synergistic fermentation with yeasts and Rhizopus oryzae had significantly enhanced ethanol concentration, umami amino acids, sweetness amino acids, and volatile compound content in sweet rice wines. The LF05-PL10 co-culture group had demonstrated the highest sensory score, umami amino acids, sweetness amino acids, higher alcohols, and ester compounds among all experimental groups, with increases of 89.03%, 94.07%, 155.37%, 335.04%, and 412.25% compared to the Rhizopus oryzae-only group, respectively. This synergistic effect had achieved the goal of “enhancing alcohol content, ester synthesis, and aroma complexity” in the fermented product. Orthogonal partial least squares-discriminant analysis (OPLS-DA) had been applied to 16 free amino acids and 73 volatile compounds in sweet rice wines. With variable importance in projection (VIP) values ≥1 as the threshold, 8 differential amino acids and 28 differential volatile metabolites had been identified as key contributors to the characteristic flavor profile of the wine. In conclusion, the cooperative fermentation strategy using Saccharomyces cerevisiae/Rhodotorula mucilaginosa with Rhizopus oryzae had effectively alleviated the bland flavor issue in Yunnan sweet rice wines, providing a theoretical foundation for flavor quality optimization in traditional fermented beverages.