This study was to study the antitumor effect of lonchocarpin (34) from traditional herbal medicine Pongamia pinnata (L.) Pierre and to reveal the underlying mechanism. The cytotoxic activities of lonchocarpin were evaluated in 10 lung cancer cell lines and it exhibited 97.5% activity at a dose of 100 μM in the H292 cell line. A field-based quantitative structure-activity relationship (3D-QSAR) study of 37 flavonoids from P. pinnata was also performed, and the results obtained showed that the hydrophobic interaction could be the crucial factor for the antitumor activity of lonchocarpin. Molecular docking studies revealed that lonchocarpin bound stably to the BH3-binding groove of the Bcl-2 protein with hydrophobic interactions with ALA146. Also, lonchocarpin significantly reduced cell proliferation via modulating Bax/Caspase-9/Caspase-3 pathway. An apoptotic test using flow cytometry showed that lonchocarpin produced about 41.1% and 47.9% apoptosis after treatment for 24 h and 48 h, respectively. Moreover, lonchocarpin inhibited tumor growth in S180-bearing mice with an inhibition rate of 57.94, 63.40 and 72.51%, respectively at a dose of 25, 50 and 100 mg/kg. These results suggest that lonchocarpin is a potentially useful natural agent for cancer treatment.