Subcritical water is an emerging method in food industry. In this study, soybean protein isolate (SPI) was treated by subcritical water (SBW) at various temperatures (0, 120, 160, 200°C) for 20 min. The changes in the appearances, physicochemical properties and structural changes were investigated. After SBW treatment, the color of SPI solution modified turned to be yellow. The mean particle size and turbidity of SPI had similar behaviors. The mean particle size was decreased from 263.7 nm to 116.8 nm at 120°C and then reached the maximum at 160°C (1446.1 nm) due to the aggregation of protein. Then it was decreased to 722.9 nm at 200°C caused by the protein degradation. SBW treatment could significantly enhance the solubility, emulsifying and foaming properties of SPI. With increasing temperature, the crystalline structure of protein was gradually collapsed. The degradation of the protein advanced structure occurred, especially at 200°C revealed by ultra-high resolution mass spectrometry. Better functional properties exhibited in hydrolysis products indicating that SBW treatment could be used as a good method to modify the properties of soy proteins isolate for specific purposes under appropriate treatment condition.