To investigate the apoptotic effect of flavonoid compound GL-V9 on human gastric cancer cells and its potential mechanism, MGC-803 and BGC-823 cells were treated with GL-V9. MTT assay was performed to assess the growth inhibition effects on MGC-803 and BGC-823 cells under different concentrations of GL-V9. Annexin V-FITC/PI staining assay was employed to observe the apoptotic rate of GL-V9 cells with the treatment of GL-V9. DAPI staining was performed to observe the nuclear morphological changes using fluorescence microscopy. Activation of caspase-9 and caspase-3 was analyzed by Western blotting. Ca2+ concentration in gastric cancer cells was detected by Fluo-3 AM staining assay. Results showed that GL-V9 could inhibitcell viability, change the nuclear morphologyl, activate caspase-9 and caspase-3 and induce the apoptosis in gastric cancer cells. The mechanism of the induction of apoptosis in MGC-803 cells under the treatment of GL-V9 may aetivate the Ca2+ associated mitochondrial apoptosis pathway.