Traditional medicine, 'LuRu', is a commonly used Tibetan medicine for clearing away heat and detoxifying. Dried products of Pedicularis flava and Pedicularis muscicola are often used as 'LuRu' in the market. This study aims to compare the chemical constituents of P. flava and P. muscicola using GC-MS and UPLC-TOF-MS, and confirm which plant species is more suitable to be used as 'LuRu'. A total of 46 and 68 compounds were identified from the volatile and non-volatile components, respectively. Out of these, 17 and 37 volatile and non-volatile components, respectively, had pharmacological activities. P. flava showed a higher content of the same active components than P. muscicola . Good biological activities are only observed in the unique components in P. flava , and not in P. muscicola . The two herbs should not be mixed in clinical medication. Our study shows that P. flava is better suited as a high-quality herb for the Tibetan medicine, 'LuRu'.