Breeding stress-tolerant industrial Saccharomyces cerevisiae strains is crucial to reduce the cost of bioethanol production. In this study, a novel strategy, atmospheric and room temperature plasma (ARTP) mutagenesis combined with genome shuffling and hybridization, was successfully applied to obtain a multiple stress-tolerant flocculating industrial S. cerevisiae strain E-158. The enhanced strain E-158 grew better under various stress conditions compared with the original strain KF-7. The concentrations of ethanol produced by strain E-158 during batch fermentation were 10.14 %-81.02 % higher than those produced by strain KF-7 under high ethanol, high temperature, and high osmosis stress conditions. The stress tolerance of E-158 kept stable even after 30 times of sub-cultivation. The lower reactive oxygen species (ROS) level and higher superoxide dismutase (SOD) and catalase (CAT) activities in strain E-158 manifested that the antioxidant defense ability of E-158 was improved and contributed to its multiple stress-tolerance. This study provided a stress-tolerant strain for industrial ethanol production and a feasible strategy for breeding multiple stress-tolerant industrial S. cerevisiae strain.