3D-QSAR, molecular docking and activity evaluation were used to study the bioactivities of ACE-inhibitory peptides with phenylalanine C-terminus. Both CoMFA (Q =0.773, R =0.992) and CoMSIA (Q =0.664, R =0.990) models were constructed. According to the established models, four novel potent ACE-inhibitory tripeptides GEF, VEF, VRF, and VKF were synthesized. The IC values were respectively determined to be 13 μM, 23 μM, 5 μM, and 11 μM by in vitro evaluation. The results show good agreement with the predicted values. The established models play an important role in revealing the structure-activity relationship of ACE-inhibitory peptides and designing novel peptides with enhanced biological activity.