Cytochrome P450 (CYP) 2C9 and CYP2C19 genetic mutant could influence the plasma concentration of glipizide in human subjects, which refers to glipizide safety and adverse effects in clinic practice. A further study to investigate the relationship of the concentrations between glipizide and its metabolites in human with different CYP mutants was valuable. We firstly develop a validated liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for simultaneous quantification of glipizide and its hydroxylated metabolites in human urine. After simple protein precipitation with methanol including 4′-OH-tolbutamide and gliclazide (both are internal standards), the analytes were chromatographed on a reversed-phased column with a mobile phase of 0.1% formic acid in acetonitrile and 0.1% formic acid in water by a gradient elution. The ion transitions of the precursor to the product ion were principally protonated ions [M + H]+ at m/z 446.4 → m/z 321.1 for glipizide, m/z 462.2 → m/z 321.1 for the four hydroxylated forms of glipizide, m/z 287.2 → m/z 188.0 for 4′-OH-tolbutamide, and m/z 324.1 → m/z 127.1 for gliclazide. The method was linear over a concentration range of 0.02–20.0 ng/mL. The intraday and inter-day variances were less than 9.9%, and accuracy was within ±6.8%. The method was successfully applied to the urinary phenotyping study in volunteers after a single oral administration of 5-mg glipizide tablet, and two new hydroxycyclohexyl metabolites of glipizide (OH-gp), 4-cis-OH-gp and 3-trans-OH-gp, were found in this study.