In order to explore the effect of Wickerhamomyces on the production of flavor compounds in Xiaoqu Baijiu, this study examined the correlation between the fungal communities in Xiaoqu and ester compounds. It was hypothesized that Wickerhamomyces contributes to the aroma of Xiaoqu. Enhanced fermentation methods were used to validate the role of Wickerhamomyces in Xiaoqu Baijiu brewing. Compared to traditional Xiaoqu, enhanced fermentation significantly increased the acidity of fermented grains and starch utilization rate (P<0.05). The fungal communities in fermented grains were analyzed by high-throughput sequencing technology. The dominant fungi in both control and test groups were Saccharomyces, Cyberlindnera, Rhizopus, and Meyerozyma, with Wickerhamomyces replacing Saccharomymycopsis in the enhanced group. Flavor compounds in the fermentation experiments were analyzed, revealing that ethyl acetate content in Xiaoqu Baijiu increased by 949.94 mg/L in the test group, while isoamyl alcohol decreased by 23.62 mg/L and isobutanol decreased by 34.81 mg/L. Functional prediction analysis using PICRUSt2 confirmed a higher relative abundance of enzymes involved in ethyl acetate metabolism and a lower relative abundance of enzymes involved in higher alcohol metabolism in the test group. These findings demonstrate that Wickerhamomyces enhances ethyl acetate production and reduces higher alcohols during Xiaoqu Baijiu brewing, offering a theoretical foundation for enhancing the quality of Xiaoqu Baijiu.