Pneumatic artificial muscles (PAMs) have many advantages such as the natural compliant, lightweight, high ratio of weight to power, thus making them an ideal choice for humanoid robots using in the rehabilitation system. However, control strategies of PAMs are facing difficulties due to their high nonlinear characteristics, uncertainties and response lag. The three-element model , which consists of a contractile element, spring element and damping element in parallel, was investigated to describe the dynamics of PAMs. To improve the trajectory tracking performance of PAM, a sliding mode control based on nonlinear disturbance observer (SMCBNDO) was applied. The experimental results show that the identified three-elements model of PAM and the SMCBNDO can achieve good accuracy of trajectory tracking controller. This work proved that this model and non-linear control method can be used for the application of the PAM-based rehabilitation system.