The present invention provides an acid-tolerant Saccharomyces cerevisiae strain and use thereof. By using exogenously added malic acid as a stress, an acid-tolerant mutant S. cerevisiae strain MTPfo-4 is obtained by directed evolution screening in the laboratory, which tolerates a minimum pH of 2.44. The mutant strain MTPfo-4, tolerant to multiple organic acids, has an increased tolerance to exogenous malic acid of up to 86.6 g/L. The mutant strain MTPfo-4 obtained is further identified. The mutant strain grows stably and well, and can tolerate a variety of organic acids (lactic acid, malic acid, succinic acid, fumaric acid, citric acid, gluconic acid, and tartaric acid). It also has a strong tolerance to inorganic acids (HCl and H3PO4). This is difficult to achieve in the existing research and reports of S. cerevisiae. The strain is intended to be used as an acid-tolerant chassis cell factory for producing various short-chain organic acids.