BACKGROUND: Soy isoflavones, structurally similar to endogenous estrogens, may affect human body through both hormonally mediated and non-hormonally related mechanisms. Heat processing could change chemical compositions. The effects of different thermal processes, boiling and HTHP(high temperature and high pressure) on the composition of isoflavone compounds and total amount of domestic soybeans were investigated in this study. METHOD AND RESULTS: Three different kinds of soybean samples were collected from RDA-Genebank. The samples were extracted using methanol, distilled water, and formic acid based solvent. Also the same solvents were used for mobile phase in UPLC/ToF/MS. All of the isoflavone compounds were analyzed based on the aglycone type of external standard for quantification. The standard calibration curve presented linearity with the correlation coefficient R2 > 0.98, analysed from 1 to 50 ppm