The acceleration of industrial development and urban expansion has led to a significant increase in flue gas emissions, posing a significant risk to human health and ecosystems. Recent studies have elucidated the significant potential of microalgae in the domain of sustainable industrial flue gas treatment. However, the inherent multifaceted factors within flue gas exert inhibitory effects on microalgal growth, thereby diminishing the overall system efficacy. Therefore, it is necessary to systematically analyze the flue gas components and propose complete intermediate treatment steps to alleviate their stressful effects on microalgae. Concurrently, to address the intrinsic limitations of the systemic functionality and enhance the applicability of microalgal biotechnology in industrial flue gas treatment, this review proposes a series of innovative solutions and strategies aimed at improving carbon fixation efficiency and lipid productivity of microalgae during flue gas treatment. In addition, the feasibility and potential limitations of these strategies in industrial applications are also discussed. Furthermore, through systematic comparative analysis, the optimal scheme and development trend of industrial flue gas emission reduction technology are explored. This comprehensive review not only establishes a theoretical foundation for the application of microalgae in industrial flue gas treatment, but also offers valuable insights for future research directions in related fields.