Phellodendri Amurensis Cortex (PAC) is a well-known herbal medicine in China with complex components, but the previous research has mostly focused on its alkaloids analysis. For the first time, a simpler and more efficient method was proposed in this paper to simultaneously determine the content of three different kinds of compounds—phenolic acids, alkaloids and limonoids—in PAC. The phenolic acids included 3-O-feruloylquinic acid, 4-O-feruloylquinic acid and syringin. The alkaloids include magnoflorine, phellodendrine, jatrorrhizine, palmatine and berberine, while the limonoids include obaculactone and obacunone. An approach combining multi-wavelength and HPLC-DAD was used in this study due to the great difference in maximum absorption wavelength of the various components. Four wavelengths at 215, 275, 280 and 310 nm, respectively, were chosen for monitoring. It has been indicated through appropriate tests that this approach is of high accuracy, good repeatability and stability and provides a scientific basis for the quality assessment of PAC and associated derivatives. In addition, the chromatographic fingerprints method combined with multivariate statistical analysis chosen in this study was proved to be effective and reasonable for an accurate classification of 33 batches of samples collected from different locations.