The objective of this study was to develop a microcapsule by the entrapment of Ainsliaeaacerifolia extract (AAE) in native starch and citrate starch matrices through spray-drying and dry heating reaction. AAE microcapsules were assessed based on recovery, encapsulation capacity, FT-IR, FE-SEM, swelling power, solubility, releasing pattern of AAE from microcapsules, and antioxidant activity. Upon increasing the addition levels of AAE and adding citric acid in the pre-emulsion mixtures, the spray-drying recovery and encapsulation capacity of AAE microcapsules increased. AAE microcapsules exhibited irregular shapes due to excessive shrinkage of their spheres. FT-IR spectra implied the formation of ester groups between starch molecules and either citric acid or phenolic compounds in AAE. Swelling powers and solubility of AAE microcapsules were significantly higher for citrate starch matrix (relative to native starch). The effects of temperature and enzyme hydrolysis on AAE releasing patterns were similar over AAE microcapsules prepared in this study. AAE microcapsules facilitated the free radical scavenging in an aqueous (relative to alcoholic) reaction system. Overall, the entrapment of AAE into the matrices from native starch and citrate starch would be one of the possible ways to expand the utilization of raw materials, by-product, and extract from Ainsliaeaacerifolia in food industries.