Heating under pressure treatment (HUP) is a method which can keep the complete form of quinoa grain after processing, which is beneficial to the development of subsequent products. The conditions for quinoa heating under pressure was optimized by response surface methodology to be: quinoa grains were regulated with adding 6.3% of pH 7.0 water and heated under 0.36 MPa pressure for 3–5 min, resulting in the predicted maxima of total phenolic content (TPC), Flavonoid and Saponin content were 313.21 mg GAE/100 g, 1.621 mg/g, and 16.78 mg/g and the values of OH Scavenging Rate, DPPH Scavenging Rate, ABST+ Scavenging Rate were 69.45, 91.73, and 52.38% separately. The content of flavonoid and saponin in the HUP samples were more than that in the boiled, baked, and extruded samples, which were close to that in raw quinoa sample, and meaning high retention of active phytochemicals and antioxidation activity in HUP quinoa. The hydroxyl radical scavenging rate is related to the content of polyphenol, flavonoid and saponin.