The bioactive components in soybeans have significant physiological functions. However, the intake of soybean trypsin inhibitor (STI) may cause metabolic disorders. To investigate the effect of STI intake on pancreatic injury and its mechanism of action, a five-week animal experiment was conducted, meanwhile, a weekly monitor on the degree of oxidation and antioxidant indexes in the serum and pancreas of the animals was carried out. The results showed that the intake of STI had irreversible damage to the pancreas, according to the analysis of the histological section. Malondialdehyde (MDA) in the pancreatic mitochondria of Group STI increased significantly and reached a maximum (15.7 nmol/mg prot) in the third week. Meanwhile, the antioxidant enzymes superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), trypsin (TPS), and somatostatin (SST) were decreased and reached minimum values (10 U/mg prot, 87 U/mg prot, 2.1 U/mg prot, 10 pg/mg prot) compared with the Group Control. The RT-PCR results of the expression of SOD, GSH-Px, TPS, and SST genes were consistent with the above. This study demonstrates that STI causes oxidative structural damage and pancreatic dysfunction by inducing oxidative stress in the pancreas, which could increase with time.