To find efficient natural antioxidants and further improve the utilization value of Nymphaea hybrid, the alcohol extracts from that are embedded and an all-round evaluation for the antioxidant activity is carried out. The microcapsule process is optimized by Box-Behnken response surface analysis which includes the wall-to-core ratio of 3.39:1, inlet air temperature at 195.56 °C, and the homogeneous number of 4.03, exhibiting the highest microencapsulation efficiency (94.36%). Antioxidant experiments in vitro showed that there was no significant difference between alcohol extracts and microcapsule on DPPH•, •O 2 and •OH, while the scavenging activity of microcapsule on ABTS + • was lower against alcohol extracts. It was worth noting that the activities of GSH, SOD and CAT in vivo were increased about 55.55%, 29.13% and 51.23%. Similar results were obtained with microcapsule treatment. The heat treatment results showed the scavenging activities of alcohol extracts and microcapsule on antioxidant experiments in vitro were all decreased; however, the antioxidant activity of microcapsule was higher than that of alcohol extracts, indicating that the microencapsulation could improve the thermal stability. In conclusion, Nymphaea hybrid alcohol extracts is a well natural antioxidants, moreover, this study provide basic support for comprehensive utilization of Nymphaea hybrid.