The hydrophobic ionic liquid of [BMIM][PF6] was successfully used for the ultrasound‐assisted extraction of hydrophobic magnolol and honokiol from cortex Magnoliae officinalis. To obtain the best extraction efficiencies, some ultrasonic parameters including the concentration of [BMIM][PF6], pH, ultrasonic power and ultrasonic time were evaluated. The results obtained indicated that the [BMIM][PF6]‐based ultrasound‐assisted extraction efficiencies of magnolol and honokiol were greater than those of the [BMIM][BF4]‐based ultrasound‐assisted extraction (from 48.6 to 45.9%) and the traditional ethanol reflux extraction (from 16.2 to 13.3%). Furthermore, the proposed extraction method is validated by the recovery, correlation coefficient (R2) and reproducibility (RSD, n=5), which were 90.8–102.6, 0.9992–0.9998, and 1.6–5.4%, respectively.