Shenling Baizhu Granule, a traditional Chinese medicine prescription comprising Renshen, Gancao, and Shanyao, has been widely consumed in China nowadays. However, its pharmacopoeia quality-marker (Q-marker) has not been defined nowadays. The study thus used a novel strategy, i.e., library-based ultra-high-performance liquid chromatography-quadrupole-orbitrap mass spectrometry, to analyze its lyophilized aqueous powder. The strategy has simultaneously and putatively 77 compounds; Especially, 32 isomeric compounds have been strictly distinguished, including ferulic acid and isoferulic acid; liquiritigenin and isoliquiritigenin; 3,4-dicaffeoylquinic acid and 4,5-dicaffeoylquinic acid; schaftoside and isoschaftoside; ginsenoside Re and ginsenoside Rd; ginsenoside Rc and ginsenoside Rb2; daidzein and 7,4’-dihydroxyflavone; luteolin and kaempferol; butin and S-naringenin; calycosin and prunetin; isovitexin and cosmosiin; orientin and quercitrin; costunolide and alantolactone; 2’-hydroxydaidzein, genistein, and apigenin; ginsenoside Rg2, 20R-ginsenoside Rg3, and 20S-ginsenoside Rg3. In addition, 45 non-isomeric compounds have been also putatively identified. Combining with the quantum chemistry calculation and UV-vis spectra scanning results, 4 compounds are recommended as pharmacopoeia Q-marker candidates, including glycyrrhizic acid, ginsenoside Re, ginsenoside Rb1, and diosgenin. The four can be used to qualitatively assess the materials of Renshen, Gancao, and Shanyao, to prevent possible adulterant.