Targeted biofortification is an effective way to regulate the microbial community succession and the production of flavor metabolites in the Baijiu fermentation. However, the high organic acid present in the Baijiu brewing process causes the gradual succession of exogenous functional microorganisms to be less dominant, ultimately resulting in defective flavor substances. In this study, a strain of Saccharomyces cerevisiae YS219 with high production of ethyl hexanoate and excellent organic acid tolerance was excavated, and the effects of this strain on the microbial composition and flavor metabolites during the fermentation of strong-flavor Baijiu were investigated. The microbial community was analyzed using the Illumina Miseq Pe300 Sequencing Platform, and at the genus level, Saccharomyces, Lactobacillus, and Pediococcus became the dominant genera after biofortification. A total of 77 flavor substances were detected in the biofortified fermented grains, and the contents of total esters and alcohols increased significantly. Among them, ethanol and ethyl hexanoate were significantly increased. Mantel test showed significant positive correlation between lactic acid and Pediococcus. Moreover, lactic acid, acetic acid, and ethanol were negatively correlated with most of the fermenting microorganisms. Following inoculation with S. cerevisiae YS219, Saccharomyces and Pediococcus exhibited a positively significant link with ethyl hexanoate, according to Spearman's correlation analysis. Taken together, the results demonstrate that the addition of S. cerevisiae with excellent organic acid tolerance and high ethyl hexanoate production helps to promote the change of microbial community and the elevation of ethanol and ethyl hexanoate.