Utilizing microalgae to capture flue gas pollutants is an effective strategy for mitigating greenhouse gas emissions. However, existing carbon-fixing microalgae exhibit poor tolerance towards acidic flue gas. In this study, the Desmodesmus sp. SZ-1, which can thrive in acidic environments and efficiently sequester CO2, was isolated. Desmodesmus sp. SZ-1 exhibited strong acid tolerance ability, with an average carbon fixation rate of 497.6 mg/L/d under 10 % CO2 and pH 3.5. Physiological analysis revealed that SZ-1 responded to high CO2 by increasing chlorophyll levels while coping with acidic stress by activating antioxidant enzymes. Genome analysis revealed a large number of carbon fixation and acid adaptation genes, involved in membrane lipid biosynthesis, H+ pumps, molecular chaperones, peroxidase system, amino acid synthesis, and carbonic anhydrase. This study provides a novel algal resource for mitigating acid gas emissions and a comprehensive genetic database for genetically modifying microalgae.