Biyan Qingdu Granules (BYQD) is a traditional Chinese medicine (TCM) formulation used to treat symptoms associated with increased secretion during nasopharyngeal carcinoma (NPC) radiotherapy. However, a comprehensive investigation into its pharmacodynamic material basis has not been conducted. This study presents a method that integrates UHPLC-HRMS and UHPLC-MS/HRMS with network pharmacology to investigate the pharmacodynamic components, multi-tissue distribution and biotransformation processes of BYQD. This study systematically identified 20 pharmacodynamic constituents in plasma following BYQD administration and characterized their distribution patterns across six tissues (heart, liver, spleen, lung, kidney, and nasopharynx). Through integrated network pharmacology and molecular docking validation, four critical bioactive components were prioritized: quercetin, jaceosidin, α-allocryptopine, and magnoflorine. Furthermore, we established the first comprehensive multi-tissue metabolic atlas for BYQD, identifying 40 phase I/II metabolites with tissue-specific metabolic signatures. These findings delineate the in vivo process of BYQD components, unravel their pharmacodynamic material basis.