A simple, rapid and green ultrasound-assisted ionic liquid solid–liquid extraction coupled with aqueous two-phase extraction method was developed and applied to the extraction of shikonin, acetylshikonin and β,β′-dimethylacrylshikonin in Arnebia euchroma (Royle) Johnst. The separation and determination of the analytes was performed by high-performance liquid chromatography coupled with diode array detection. In the study, 1-butyl-3-methylimidazolium tetrafluoroborate ([C4MIM][BF4]) was used as extraction solvent. Ionic liquid-based solid–liquid extraction and aqueous two-phase extraction were performed simultaneously in one tube under the assistance of ultrasound. The liquid–liquid–solid three-phase system, namely surfactant-rich phase, water-rich phase and sample-rich phase, was formed. The target analytes were enriched in the surfactant-rich phase. Under the optimal experimental conditions, the calibration curves of target analytes showed good linear relationship (r > 0.9997). The inter-day and intra-day precision were in the range of 3.42–8.53 and 1.98–3.14%, respectively. The LOD and LOQ for the target analytes were in the range of 5.0–19.2 and 16.7–64.2 ng mL−1, respectively. The recoveries of naphthoquinone pigments ranged from 90.00 to 97.73% and relative standard deviations were less than 4.50%. Compared with heat reflux extraction and ultrasonic-assisted extraction, the proposed method is simpler, faster and more effective, because the mass transfer process for the analytes was always performed in one centrifugal tube and the steps such as filtration, concentration and redissolution were avoided. The present method was demonstrated to be efficient and satisfactory for the extraction of naphthoquinone pigments in medicinal plants.