Strong-flavor Baijiu is a typical representative of traditional Chinese distilled alcoholic beverages, with a long history and unique flavor. Flavor analysis showed that fatty acid ethyl esters have a key influence on the sensory properties of strong-flavor Baijiu. Esterification reaction catalyzed by ester synthases from microorganisms is an important way to synthesize fatty acid ethyl esters using alcohols and acids as the substrates. However, the mechanism of enzymatic catalysis is not clear until now, and leads to the batch instability for synthesizing esters in strong-flavor Baijiu during fermentation process. The classical enzyme catalyzed esterification of acids and alcohols is under organic phase system, while the water content of fermented grains is 53% ~58% during Baijiu fermentation. It is generally recognized as a water phase system. Identifying enzymes for synthesizing fatty acid ethyl esters and revealing the catalytic mechanism can provide a theoretical basis for improving the quality of strong-flavor Baijiu. Baijiu flavor esters and microbial metabolism were summarized in this review. The structure and catalytic mechanism of microbial enzymes from Baijiu were also discussed to provide a scientific basis for clarifying the synthetic mechanism of ethyl esters in strong-flavor Baijiu.