In this study, a preparative separation method was established to simultaneously isolate the polymethoxylated flavones (PMFs) from the peel of “Dahongpao” tangerine using macroporous adsorptive resins (MARs) combined with prep-HPLC. The total PMFs were enriched using MARs to remove most sugars, water-soluble pigments, and flavanones, and the eluents obtained were analyzed by ultra-performance liquid chromatography (UPLC) to determine the PMF composition. The separation and purification of PMFs were carried out by using a mass spectrometry-guided prep-HPLC with a gradient elution of acetonitrile-water (v/v), simultaneously. The purity of these PMFs was determined by UPLC, and their chemical structures were confirmed by electrospray ionization mass spectrometry (ESI-MS-MS), ultraviolet (UV), and nuclear magnetic resonance (NMR). Using the present method, five PMFs, including 5,6,7,4’-tetramethoxyflavone (1), nobiletin (2), tangeretin (3), sinensetin (4), and 5-hydroxy-6,7,8,3’,4’-pentamethoxyflavone (5), can be purified simultaneously, and the purity of the compounds obtained were 95.3%, 99.7%, 99.5%, 98.9%, and 98.1%, respectively. The method reported here is simple, rapid, and efficient, and it can be used to separate PMFs from citrus fruit peels and, potentially, other plant materials.