Abstract: We identified molecular mechanisms by which Isatidis Radix might prevent or mitigate influenza and corona virus disease 2019 (COVID-19) based on chemical composition and network pharmacology. High performance liquid chromatography coupled to tandem quadrupole time-of-flight mass spectrometry (HPLC-Q-TOF-MS) was used to analyze the components of Isatidis Radix. Seventy compounds were identified, of which 33 prototype compounds entered the blood. Network pharmacological analysis of 41 potential active components demonstrated that Isatidis Radix can regulate protein kinase B1 (AKT1), serum albumin (ALB), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), vascular endothelial growth factor A (VEGFA), tyrosine-protein kinase SRC (SRC), epidermal growth factor receptor (EGFR), intercellular adhesion molecule-1 (ICAM1) and other key genes, which have preventive effects on influenza and COVID-19 through hypoxia inducible factor-1 (HIF-1), vascular endothelial growth factor (VEGF), tumor necrosis factor (TNF), influenza A, Toll-like receptor (TLR), phosphatidylinositol-3-kinase-protein kinase B (PI3K-AKT), COVID-19 and other signaling pathways. This study identifies mechanisms by which Isatidis Radix might act against influenza and COVID-19 that are related to the inflammatory response, immunomodulation and viral defense, and provides a basis for subsequent clinical research. All animal experiments were approved by the Ethics Committee of Shenyang Pharmaceutical University (SYPU-IACUC-S2020-12.23-201).