In order to improve the storage stability and extend the application range of the Abelmoschus Manihot (L.) medic flowers flavonoids(AMF), A.Manihot flowers flavonoids microcapsules (AMFM) were prepared by ultrasonic-assisted embedding-freeze drying method with the flavonoids extracts of AMF as core material and β-cyclodextrin as wall material. The preparation parameters of microcapsules were determined by single factor and response surface test, and AMFM was characterized by scanning electron microscopy, infrared spectroscopy and antioxidant activities. The effects of different storage conditions of temperature, humidity, light and oxygen on the retention rate of the microcapsules were investigated. The results show that the optimal preparation process of AMFM is ultrasonic power of 210 W, ultrasonic temperature of 56 ℃, ultrasonic time of 40 min and core-wall ratio of 1.6 mL∶1 g. Under these conditions, the flavonoid embedding rate of microcapsules was 96.89%. The prepared microcapsules are amorphous glassy solids, and the infrared spectrum analysis shows that the AMF are embedded by the wall material. AMFM has good antioxidant capabilities and can effectively improve the stability of flavonoids. This study provides a theoretical basis for the development of AMF for the application of new food natural antioxidants.