Three quinoa （black quinoa， red quinoa and yellow quinoa） were researched by the simulated in vitro digestion to investigate the changes of polyphenols， flavonoids and antioxidant properties. The results showed that the total polyphenol content （TPC） was black quinoa > red quinoa > yellow quinoa （P<0.05）， and total flavonoids content （TFC） was red quinoa > black quinoa > yellow quinoa（P<0.05）. After simulated in vitro digestion， the mouth， stomach and small intestine can significantly promote the release of polyphenols and flavonoids （P<0.05）. Iron reduction/antioxidant capacity （FRAP） and ABTS+ free radical scavenging capacity were approximately as follows： oral > small intestine > stomach > large intestine （P<0.05）， and antioxidant capacity showed significant positive correlation with polyphenols and flavonoids in quinoa. After digestion in vitro， the binding polyphenolic compounds（gallic acid， ferulic acid， etc.） in quinoa were significantly released， showing higher biological activity， so that it has a higher nutritional health value.