The detection of emerging contaminants (ECs) and understanding their ecotoxicity has brought new challenges to water pollution control. Triclosan (TCS), as an emerging contaminant, is a commonly used antibacterial agent widely present in the environment. Microdialysis (MD), as a sampling technique, can overcome some of the deficiencies of traditional approaches to sampling, using sources such as blood, urine, tissue, and target organs, in terms of invasiveness, time from collection to analysis, and possible changes during sample preparation. In this study, we coupled MD with analysis using UHPLC-QTOF/MS to identify the endogenous metabolites in the liver as biomarkers of the exposure of living crucian carp to TCS. The identified biomarkers were then quantified using UHPLC-MS/MS to continuously monitor the effect of TCS on endogenous metabolites in the liver of living crucian carp, which contributes to a better understanding of the toxicological effect of TCS. The experimental results demonstrated that TCS exposure interfered with the metabolic pathways of amino acids (L-isoleucine and L-histidine), purines (xanthine and hypoxanthine), and small nerve molecules (acetylcholine and choline).