Natural antioxidants are widely used in the life sciences. Phellinus igniarius is a historically used natural antioxidant containing a variety of active compounds. Phenols, particularly Inoscavin A and Hypholomine B, are found in the high concentrations. Better quantitative methods are needed to perform quality control in order to support further research of this mushroom. An ultra-performance liquid chromatography method coupled to photodiode-array detection and an electrospray ionization tandem mass spectrometry method (UPLC-PAD-MS) was developed to simultaneously quantify Inoscavin A and Hypholomine B levels in the medicinal fungus Phellinus igniarius. The two compounds were quantified using UPLC-PAD and UPLC-MS. The methods were accurate (mean accuracy for spiked matrix ranged from 101.5% to 105.8%), sensitive (limit of detection ranged from 0.28 to 1.14 mg L-1) and precise (the relative standard deviations ranged from 0.13 to 2.8%). Inoscavin A and Hypholomine B were purified using high-speed counter-current chromatography (HSCCC), structural evaluated to meet the request of standard substances. UPLC separation was performed on a reversed-phase C18 column using gradient elution with acetonitrile and 0.1% formic acid over 10 min. The developed method was successfully applied to determine Inoscavin A and Hypholomine B in twelve Phellinus igniarius samples of different origins and the results showed that it was suitable for the analysis of these active components in Phellinus igniarius samples.