Abstract: The aim of this study was to identify the anti-inflammatory markers of Zhachong shisanwei pills (ZC-13) and characterize their mechanisms. UPLC/Q-TOF-MS combined with an NF-κB dual fluorescence reporter gene system and NO content detection were utilized to identify the anti-inflammatory bioactive substances in ZC-13. Network pharmacology and bioinformatics methods were used to predict the main targets and pathways of these anti-inflammatory markers, and to verify the main anti-inflammatory pathways of costunolide. Results showed that in ZC-13, four kinds of markers related to NF-κB inhibition were identified: gallic acid, ellagic acid, liquiritin apioside, glycyrrhizic acid, and four kinds of markers related to NO release inhibition were found: gallic acid, liquiritigenin, costunolide, and dehydrocostus lactone. The above components exert anti-inflammatory activities mainly through the regulation of PDK1 (3-phosphoinositide-dependent protein kinase 1), MAPK14 (mitogen-activated protein kinase), GSK3β (glycogen synthase kinase-3β) and other anti-inflammatory-related targets, and further adjust the PI3K-AKT (phosphoinositide 3-kinase- protein kinase B), MAPK, mTOR (mammalian target of rapamycin) pathways. Among them, costunolide can inhibit AKT phosphorylation and NF-κB nuclear transfer. The above results identified the anti-inflammatory markers and possible mechanisms of ZC-13, and provide a theoretical basis for standardizing the clinical application and quality of ZC-13.