Abstract: The molecular forces involved in the enzymatic coagulating process of soyabean protein isolate(SPI) by an alkaline proteinase Alcalase were investigated by adding different chemical reagents. Results indicate that non-covalent bonds, including hydrogen bond and hydrophobic reaction contribute most to the coagulating reaction, while ionic bond and disulfide bond have little effect on the coagulating process. Depending on secondary chemical bonds and having to resist to the repulsive interaction by the negative charges may explain why the coagulating strength of SPI coagulum induced by Alcalase is weaker than that induced by acid and saline coagulants. The current screening strategy for soymilk coagulating enzymes is also commented according to the results.