Ultra performance LC with quadrupole TOF MS (UPLC/Q-TOF-MS) fingerprinting is first developed for the identification of the major components of Phellodendri Amurensis Cortex (PAC). The PAC samples are separated using a Waters ACQUITY UPLC BEH C18 (2.1×50 mm, 1.7 μm) by linear gradient elution using water (containing 0.2% formic acid) and acetonitrile (containing 0.2% formic acid) as the mobile phase. Ten batches of PAC are selected to construct the UPLC/Q-TOF-MS fingerprint. Sixteen common peaks in the fingerprint are obtained, ten of which are tentatively identified, with reference to the literature data, as phellodendrine, magnoflorine, tetrahydropjatrorrhizine, menisperine, tetrahydropalmatine, jatrorrhizine, palmatine, berberine, obacunone, and limonin. Chemometric methods are also employed to evaluate the variation of herbal drugs and other closely related herbs based on the characteristics of peaks in the UPLC/Q-TOF-MS profiles. The developed fingerprint assay is a powerful method that may be used to conduct quality control of PAC.