This study aims to develop a leveling position control of an active PWM-controlled pneumatic isolation table system. A novel concept using parallel dual-on/off valves with PWM control signals is implemented to realize active control and to improve the conventional pneumatic isolation table that supported by four pneumatic cushion isolators. In this study, the cushion isolators are not only passive vibration isolation devices, but also pneumatic actuators in active position control. Four independent closed-loop position feedback control system are designed and implemented for the four axial isolators. In this study, on/off valves are used, and PWM is realized by software. Therefore, additional hardware circuit is not required to implement PWM and not only cost down but also reach control precision of demand. In the controller design, the Fourier series-based adaptive sliding-mode controller with H∞ tracking performance is used to deal with the uncertainty and time-varying problems of pneumatic system. Finally, the experiments on the pneumatic isolation table system for synchronous position and trajectory tracking control, including no-load and loading conditions, and synchronous position control with master-slave method, are implemented in order to verify that the controller for each cushion isolator can realize good position and trajectory tracking performance.