Taking Phellodendron chinense Schneid (PcS) as the raw material with ultrasonic-assisted eutectic solvent, the effects of various DESs on the extractable content of palmatine and berberine in PcS were investigated. On the basis of the single-factor test, the best DES was determined to be choline chloride and 1,3-propanediol (mole ratio 1 : 2). After optimizing by the response surface method, the optimum extraction conditions were as follows: the solid-liquid ratio was 1 : 30 (w/v), water content was 30% (v/v), vortex time was 7 min, ultrasonic time was 20 min, ultrasonic temperature was 60°C, ultrasonic power was 400 W, and the content of palmatine in PcS was 5.421 ± 0.283 mg/g, and the content of berberine in PcS was 15.573 ± 0.539 mg/g. Therefore, DES prepared from choline chloride and 1,3-propanediol can be used to extract palmatine and berberine from PcS. The optimized process conditions determined by the response surface method are reliable and can provide a reference for the green extraction of effective components from PcS.