Abstract <p>With the acceleration of industrialization and the emergence of increasingly complex environmental pollution issues, conventional single-pollutant treatment technologies have gradually revealed limitations such as low efficiency and poor adaptability. As photosynthetic autotrophic microorganisms with flexible metabolism and multi-target pollutant absorption and transformation capabilities, photosynthetic microbes demonstrate unique advantages in wastewater treatment, air pollution control, and carbon dioxide fixation. In recent years, research on the synergistic removal of pollutants-such as heavy metals, organic contaminants, and nutrients-has evolved from macro-scale engineering optimization to in-depth exploration of molecular mechanisms and regulatory networks. This review systematically summarizes the principal molecular mechanisms employed by these cells, including cell-surface adsorption, ion uptake mediated by transmembrane transporters, enzyme systems associated with organic compound degradation, regulation of photosynthetic and heterotrophic metabolism, antioxidant defense systems, and signal transduction pathways. Furthermore, global transcriptomic, proteomic, and metabolomic response patterns under multipollutant stress are analyzed to elucidate the transcription factors and signaling networks governing key metabolic nodes. Advances in enhancing removal capacity through genetic engineering and synthetic biology are highlighted, along with prospects for integrating multi-omics and systems biology into remediation systems. This review aims to provide a theoretical foundation and future research directions for molecular-level optimization and industrial application of biological remediation technologies.</p> Graphical Abstract