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Low frequency sonophoresis (LFS) is currently being attempted as a transdermal drug delivery method in clinical areas. However, it lacks both an effective control method and the equipment to satisfy the varying drug dosage requirements of individual patients. Herein, a novel method aimed at controlling permeability is proposed and developed, using a pressure control strategy which is based on an accurate, adjustable and non-invasive ultrasound transdermal drug delivery system in in vitro LFS. The system mainly consists of a lead screw linear ultrasonic motor and an ultrasonic transducer, in which the former offers pressure and the latter provides ultrasound wave in the liquid. The ultrasound can enhance non-invasive permeation and the pressure from the motor can control the permeability. The calculated and experimental results demonstrate that the maximum pressure on artificial skin is under the area with the maximum vibration amplitude of the ultrasonic transducer, and the total pressure consists of acoustic pressure from the transducer and approximate static pressure from the motor. Changing the static pressure from the ultrasonic motor can effectively control the non-invasive permeability, by adjusting the duty ratio or the amplitude of the motor’s driving voltage. In addition, the permeability control of calcein by thrust control is realized in 15 min, indicating the suitability of this method for application in accurate medical technology. The obtained results reveal that the issue of difficult permeability control can be addressed, using this control method in in vitro LFS to open up a route to the design of accurate drug delivery technology for individual patients.