This study aimed to investigate the purification of radioactive thorium (Th4+) by Chlorella vulgaris in aquatic environments. Single-factor experiments and response surface optimization tests identified optimal purification conditions. The purification and metabolic response mechanisms of Chlorella to Th4+ were elucidated using physiological and biochemical analyses, three-dimensional excitation-emission matrix (3D-EEM) analysis, and metabolomic profiling. Increases in the Th4+ concentration caused Chlorella to self-flocculate, significantly improving the Th4+ purification efficiency. Under optimal conditions, the Th4+ purification efficiency for Th4+ in wastewater by Chlorella stabilized between 94.3 % and 98.2 %. Morphological analysis revealed that the purified Th4+ existed mainly in a stable residual state. Chlorella efficiently purified wastewater during treatment by regulating environmental pH, performing redox reactions, and utilizing extracellular polymeric substances (EPS) to interact with Th4+. Metabolomic analysis indicated that Chlorella adapted to the Th4+-contaminated environment and enhanced its purification function by adjusting the synthesis of metabolites, such as carbohydrates, nucleotides, and amino acids. Chlorella demonstrated a remarkable self-flocculation phenomenon and a high-efficiency purification capability for Th4+, offering new possibilities for environmental remediation. Its purification mechanism involves environmental regulation, redox reactions, and complex metabolic adjustments. The results presented here provide theoretical support for environmental remediation using Chlorella.