Tributyltin chloride (TBT-Cl), one of the most representative chemical compounds of tributyltin (TBT), is a threat to aquatic organisms due to evidence of fatal toxicity, which has attracted much interest in the scientific community. We studied the effects of acute TBT-Cl exposure on the juvenile Takifugu obscurus metabolism by investigating the metabolite contents in the serum and liver at three TBT-Cl concentrations and in a control group using the LC-MS technology. The metabolites that showed different levels in the serum and liver under different TBT-C1 concentrations were primarily related to sphingolipid metabolism, phosphoglyceride metabolism, and the biosynthesis of unsaturated fatty acids. Moreover, we found that TBT-Cl exposure increased the concentration of lysophosphatidylcholine and prostaglandin E₂, resulting in higher detoxification capacity and inhibiting inflammation. These results may explain the higher tolerance of juvenile T. obscurus to TBT-Cl compared with other fish species. Overall, the present study contributes new information of the influences of TBT-Cl on juvenile T. obscurus metabolism.