The extraction of functional components from radix of Arnebia euchroma was optimized using orthogonal design based on the extraction yields of shikonin, and hydroxyl-naphthoquinone pigments. The data processing was carried out with the multiple guidelines grading method for optimizing the extraction condition. Compared with the traditional method (refluxing and ultrasonic extraction), the flash extraction method was more efficient The optimal conditions were as follows: 95% ethanol extract 3 times with 90 s for each. Under these conditions, the extraction yields of shikonin, and hydroxyl-naphthoquinone pigments were 93.16%, 93.89%, respectively, and the dry extract rate was 5.16%. In conclusion, the result showed that the flash extraction technology was appropriate, stable and feasible.