BACKGROUND: β-cypermethrin (β-CYP) exhibits high toxicity to aquatic organisms and poses significant risks to aquatic ecosystems. , a protozoa widely distributed in aquatic environments, can tolerate high concentrations of β-cypermethrin. However, the comprehensive detoxification mechanisms remain poorly understood in . METHODS: Untargeted metabolomics was used to explore the detoxification mechanisms of under β-CYP stress. RESULTS: Trehalose, maltose, glycerol, and D-myo-inositol were upregulated under β-CYP exposure in . Furthermore, the expression level of was upregulated under β-CYP treatment. knockout mutants resulted in a decreasing proliferation rate of under β-CYP stress. The valine-leucine and isoleucine biosynthesis and glycine-serine and threonine metabolism were significantly affected, with significantly changed amino acids including serine, isoleucine, and valine. CONCLUSIONS: These findings confirmed that develops β-CYP tolerance by carbohydrate metabolism reprogramming and Cyp5011A1 improves cellular adaptations by influencing amino acid metabolisms. Understanding these mechanisms can inform practices aimed at reducing the adverse effects of agricultural chemicals on microbial and environmental health.