Ovomucoid (OVM) is a critical anti-nutritional factor in egg, which may reduce nutrient utilization. In this study, the effects of polyphenols on the trypsin inhibitory activity (TIA) of OVM were investigated by exploring the structural changes and interaction mechanisms. The results found that TIA decreased to 62.34% and 90.41% as epigallocatechin gallate (EGCG) and gallic acid (GA) were added individually. EGCG and GA interacted with OVM via static quenching and hydrophobic interaction. They induced a transition of OVM conformation from disorder to order. Infrared and fluorescence quenching analysis showed that the interaction between EGCG or GA and OVM was spontaneous, and hydrophobic interaction was the predominant force. The mechanism suggested that polyphenols affect the protein conformation by spontaneously binding to OVM in hydrophobic interactions, and lowering the TIA through reduced hydrophobicity. In summary, EGCG may be a promising OVM trypsin activity inactivator, which could also guarantee safety of egg products.