Yi-Shen-Hua-Shi (YSHS) Granule is a well-known patented herbal drug for treating chronic glomerulonephritis (CGN) in China. Its chemical compositions and anti-CGN components are not fully understood. This study aimed to establish the chemical profile and to identify the anti-CGN components of YSHS Granule. For these purposes, a HPLC-Q-TOF-MS/MS method was developed. A total of 105 peaks were detected in the mass spectrum of the Granule. Of these, 99 compounds were tentatively identified as terpenoids, flavonoids, coumarins, alkaloids, phenols, and other types of compounds, and 15 were further identified with reference substances. To screen bioactive compounds, a cell membrane immobilized chromatography (CMIC) method was used. Lipopolysaccharide (LPS)-challenged rat glomerular mesangial cells (HBZY-1) were incubated with YSHS Granule (100 μg/mL), and the binding components to the cell membrane were extracted and analyzed using the established HPLC-Q-TOF-MS/MS method. Seven potential bioactive components that bound to HBZY-1 cell membranes were detected and identified as calycosin-7-O-β-D-glucoside, 6-gingerol, naringin, ginsenoside Re, poncirin, liquiritigenin, and isoliquiritigenin. The outcomes of the present study provide a chemical basis for clinical use of the Granule in managing CGN, and provide quality control markers for the Granule’s production and use.