Squalene synthase (SQS) inhibitors were screened from various plants and food extracts. Effective SQS inhibitor was purified from fermented soybean paste using ethanol extraction, HP-20 column chromatography, ethyl acetate extraction, silica gel column chromatography, and crystallization. Through UV spectrometry, $^1H$ NMR, $^{13}C$ NMR, and mass spectrometry, SQS inhibitor was identified as daidzein with molecular mass of 254 and molecular formula of $C_{15}H_{10}O_4$. Daidzein showed $IC_{50}$ value of 50 nmol/L against SQS, confirming its potential as therapeutic agent for hypercholesterolemia.