Cyanidin 3-rutinoside is an important anthocyanin which has good antioxidant activity and beneficial health effects. It was prepared from litchi fruit pericarp by ultrasound-assisted extraction and purified in this work. A mathematical model was built between ultrasonic power, time, ethanol concentration and cyanidin 3-rutinoside yield. The R², P-values of model and “lack of fit” indicated the high fitness of the model to true behavior. Every factor showed evident effects and interactions on the cyanidin 3-rutinoside yield. The optimal conditions to obtain the highest yield of cyanidin 3-rutinoside were 240 W of ultrasonic power, 34.5 min of ultrasonic time and 54.1% of ethanol concentration. The predicted yield of cyanidin 3-rutinoside was not significantly (p > 0.05) different to the practical value conducted under optimal conditions.