By evaluating the results of treating quinoa with different microwave conditions, this paper compares the effects of microwave heating and traditional conduction heating (water bath and baking) on lipase and flavor components of quinoa. Experiments results show that with the increase of microwave power and the extension of treatment time, the activity of lipase decreased significantly. After heating at 600 W power for 4 min, the lipase activity tended to be stable. Through analyzing flavor components in quinoa, we found microwave treatment dramatically reduced the levels of Methyl Ketone, 1-octen-3-ol and trans-2-Nonenal. Moreover, with the extension of storage time, the oxidation of oil in quinoa was inhibited by microwave, with the peroxide value and acid value of quinoa decreased. Compared with the traditional heating methods, microwave heating can significantly reduce the activity of lipase in quinoa, and improve the flavor and organoleptic attribute of quinoa milk.