Natural betalains can be potential food additives because of their antioxidant activities, but they have poor thermal stability. In this study, betalains were extracted from red dragon fruit peel, and then encapsulated with maltodextrin by ultrasound method to increase the physicochemical properties of betalains microcapsules. The encapsulation efficiency of the betalains was above 79%, and the particle size and Zeta potential values were 275.46 nm and -29.01 mV, respectively. Compared to the control sample, onset temperature and DPPH free radical scavenging of betalains microcapsules under the modest ultrasound treatment (200 W, 5 min) was increased by 1.6 °C and 12.24%, respectively. This increase could be due to the ability of ultrasonification to create interactions between maltodextrin and betalains (as evidenced by FT-IR). Therefore, modest ultrasound treatment can be used for microcapsulation to improve the stability of betalains, and then expand the application of betalains in heat processed food field.