This paper addresses the tracking control for an n-link flexible-joint robot system with full-state constraints and external disturbances. First, a nonlinear disturbance observer (NDO) is introduced to asymptotically estimate and suppress the influence of the related disturbances. Next, the constrained system under consideration is transformed into a new unconstrained system using state-dependent function (SDF) transformations. Subsequently, a NDO-based tracking controller that combines the backstepping method and filter technique is proposed in this work. Based on stability analysis, it can be proven that the tracking error converges to a predefined compact set, which can be arbitrarily small without violating the full-state constraints. Finally, simulation results are presented to demonstrate the validity of the suggested control algorithm.