The importance of soy products in reducing the risk of cardiovascular disease is well documented. Our previous computation study has indicated the presence of several potent ACE inhibitory peptides from soybean proteins which needs to be identified. The aim of the study was to identify ACE inhibitory peptides from soy proteins using LC-MS/MS coupled with quantitative structural-activity relationship (QSAR) model. Soybean protein hydrolysate digested by thermolysin showed an IC50 value of 53.6 μg/mL, decreased slightly to 51.8 μg/mL after adding pepsin, and increased to 115.6 μg/mL after adding trypsin. A total of 34 peptides were characterized from LC-MS/MS. Five novel tripeptides, IVF, LLF, LNF, LSW and LEF, with predicted IC50 values lower than 10 μM were synthesized and validated. The results showed that soybean is an excellent source for ACE inhibitory peptides and more potent ACE inhibitory peptides are yet to be purified from soybean protein.