In this study, an efficient strategy developed by integrating UPLC-Q/TOF-MS, network pharmacology, and molecular simulation, was proposed and applied for rapidly screening bioactive candidates from ginger. A UPLC-Q/TOF MS-guided isolation targeting non-volatile pungent compounds resulted in the isolation and identification of 19 compounds in the rhizome of Zingiber officinale, including six new compounds (1-6). Based on target prediction and Gene Ontology (GO), the primary biological function of compounds was predicted to be associated with cancer and the key target was VEGFR2 (vascular endothelial growth factor receptor 2). Moreover, cytotoxic activity assays demonstrated that the isolated compounds had potential anti-proliferative effects on MDA-MB-231, A549 and HCT116 cells. In particular, compounds 7 and 8 exhibited the highest cytotoxicity against HCT116 compared with the other cell lines, with IC50 values ranging from 4.70 to 7.40 μM. In addition, VEGFR2 inhibition of compounds 7 and 8 was validated based on enzyme activity assays and their interaction mechanisms were illuminated through molecular simulations. These experimental data are consistent with the calculated results, indicating the veracity of the proposed method. In conclusion, the integrated strategy is a quick and efficient way to explore bioactive compounds as well as research the possible targets, providing us with a good possibility of screening new lead compounds from natural sources.