To explore the molecular mechanisms of the toxicity of inorganic arsenic on Portunus trituberculatus, we exposed adult female P. trituberculatus to 0.3 mg/L As³⁺ and 0.3 mg/L As⁵⁺ for 96 h. The non-targeted metabolomics method was used to compare and analyze the changes in the composition and content of metabolites in gill tissue. Compared with the control group, a total of 100 and 59 differential metabolites were obtained in the As³⁺ and As⁵⁺ exposure groups, respectively. According to the physiological functions of the afore-mentioned metabolites and the analysis of their corresponding metabolic pathways, it is speculated that As³⁺ upregulates proline, arginine, ornithine, lysine and other amino acids, and eicosanoids, glycerophospholipids, and other lipids, leading to disruptions in ABC transporter, amino acid metabolism, arachidonic acid metabolism, digestion and absorption, and aminoacyl tRNA biosynthesis. Toxic effects occur as a result, with As⁵⁺ causing abnormal metabolism of vinyl acetylglycine, N2-γ-glutamyl glutamine, γ-glutamyl glutamate, asparagine-isoleucine, glutamyl isoleucine, prolyl phenylalanine, interference with ABC transporter, amino acid metabolism, and glutathione metabolism. The observations of these toxic effects on P. trituberculatus provide a theoretical basis for future in-depth investigations of the mechanisms resulting from toxic exposure to inorganic arsenic.