Pneumatic cylinders are one kind of low cost actuation sources which have been applied in industrial and robotics field, since they have a high power/weight ratio, a high-tension force and a long durability. To overcome the shortcomings of conventional pneumatic cylinders, a number of newer pneumatic actuators have been developed such as McKibben Muscle, Rubber Actuator and Pneumatic Artificial Muscle (PAM) Manipulators. However, some limitations still exist, such as the air compressibility and the lack of damping ability of the actuator bring the dynamic delay of the pressure response and cause the oscillatory motion. In addition, the nonlinearities in the PAM manipulator still limit the controllability. Therefore, it is not easy to realize motion with high accuracy and high speed and with respect to various external inertia loads. To overcome these problems, a novel controller which harmonizes a phase plane switching control method (PPSC) with conventional PID controller and the adaptabilities of neural network is newly proposed. In order to realize satisfactory control performance a variable damper, Magneto-Rheological Brake (MRB), is equipped to the joint of the robot. The mixture of conventional PID controller and an intelligent phase plane switching control using neural network (IPPSC) brings us a novel controller. The experiments were carried out in a robot arm, which is driven by two PAM actuators, and the effectiveness of the proposed control algorithm was demonstrated through experiments, which had proved that the stability of the manipulator can be improved greatly in a high gain control by using MRB with IPPSC and without regard for the changes of external inertia loads.