•A simple and quick method for low TIA soymilk is supplied.•Heat-induced KTI incorporation into protein aggregates causes KTI’s TIA loss.•Heat-induced peptide bond cleavage of BBI causes BBI’s TIA/CIA loss.•NaCl accelerates protein aggregate formation and peptide bond cleavage of BBI. Trypsin inhibitor activity (TIA) is an important antinutritional factor in soymilk. In this study, the effects of NaCl preaddition on TIA and the heat-induced TIA inactivation mechanisms were examined. The results showed that Kunitz trypsin inhibitor (KTI) and Bowman-Birk inhibitor (BBI) contributed 74% and 26% to raw soymilk TIA, respectively. The heat-induced quick KTI incorporation into protein aggregates was the reason for its quick TIA inactivation. The heat-induced slow cleavage of one BBI peptide bond was the reason for its slow TIA inactivation. Heat-induced protein aggregate formation had little effect on BBI inactivation owing to the fact that BBI and its degradation product tended to remain in the supernatant (197,000g, 1h) in all conditions used in this study. NaCl could accelerate the KTI incorporation into protein aggregates and the cleavage of one BBI peptide bond, which supplied a simple and quick method for low TIA soymilk processing.