Carboxylic enantiomers are prevalent in living organisms and synthetic samples that exhibit important biological properties. The profiling of carboxylic enantiomers is beneficial for monitoring physiological states and further unraveling the metabolism mechanisms between carboxylic enantiomers and diseases. In this study, pairs of light and heavy isotope reagents, (S)-(3-aminopiperidin-1-yl) phenyl-methanone/d5-(S)-(3-aminopiperidin-1-yl) phenyl-methanone (APMA/d5-APMA), were synthesized and applied to tag the enantiomers of carboxylic metabolites and drugs. The tagging reagents of APMA and d5-APMA carry chiral amine groups that can efficiently and selectively react with the carboxyl group on carboxylic enantiomers. Upon the tagging strategy, pairs of carboxylic enantiomers showed satisfactory chromatographic performance on the conventional reversed-phase (RP) column, and the detection sensitivities of mass spectrometry (MS) analysis were also elevated. The obtained limits of detection (LODs) of 16 carboxylic enantiomers were in the range of 0.008–0.08 ng mL–1. With the developed method of APMA/d5-APMA tagging-assisted liquid chromatography–mass spectrometry (LC–MS) analysis, we successfully achieved the sensitive detection of carboxylic enantiomers in trace amounts of serum samples. The results showed that the levels of 6 carboxylic enantiomers in hepatic fibrosis serum presented significant alteration compared with normal serum samples. This proposed method provides great potential for uncovering the biological function of carboxylic enantiomers in the development of diseases.