A new ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) method was developed for the determination of mequindox (MEQ) and its two metabolites (1-desoxymequindox and 1, 4-bisdesoxymequindox, 1-DMEQ and BDMEQ) in swine liver. This method was validated on the basis of Commission Decision 2002/657/EC. Target analytes were extracted from swine liver with acid acetonitrile, purified by an Oasis MAX cartridge, and separated by UPLC. The chromatography total time was less than 8 min with gradient elution of 0.1% formic acid in methanol. Data acquisition was carried out by electrospray ionization tandem mass spectrometry (ESI/MS/MS) operated in a multiple reaction monitoring mode. At fortified levels from 2 to 100 μg kg−1 in swine liver, recoveries of target analytes ranged from 80% to 85% with the intra-day coefficient of variation (CV) being ≤ 14.48% and inter-day CV ≤ 14.53%, respectively. The limit of detection (LOD) ranged from 0.58 to 1.02 μg kg−1 and the limit of quantification (LOQ) range was 1.93 to 3.40 μg kg−1 for each analyte. The result indicated that this method was specific, sensitive, and suitable for the quantification and conformation of MEQ and its two metabolites in swine liver.