The high concentration of lactic acid produced during the solid fermentation of Chinese Baijiu inhibited the growth and metabolism of Saccharomyces cerevisiae, thus affecting the flavor and quality of Baijiu. This study employed a combination of Atmospheric and room temperature plasma (ARTP) and Automatic high-throughput microbial microdroplet culture system (MMC) to screen S. cerevisiae capable of tolerating high concentrations of lactic acid. The results demonstrated that the growth rate, cell integrity, ethanol production capacity and volatile aroma components content of the three lactic acid-tolerant strains were significantly superior to original strain S. cerevisiae NCUF309.5 under the stress of 4% lactic acid concentration. Especially, the acid tolerance of S. cerevisiae NCUF309.5-44 obtained through ARTP treatment and adaptive laboratory evolution by MMC, which exhibited a 93.65% increase in OD value and a 2.29-fold increase in ethanol content after 24 h of 4% lactic acid stress, remained stable after 10 consecutive sub-cultures. Besides, the content of volatile compounds increased 60.69%. In summary, this paper provided a novel screening strategy for lactic acid-tolerant S. cerevisiae and established a foundation for the selection and breeding of microorganisms used in solid-state Baijiu fermentation.