This paper presents an alternative control method based on a new unknown input observer (UIO) for servo motor systems with unknown time-varying nonlinear dynamics and disturbances. By defining auxiliary filtered variables, an invariant manifold is derived and used to design the estimation of unknown dynamics. The new observer has only one scalar to be set, and thus can be easily incorporated into the control design to achieve precise output tracking. The convergence of the proposed estimator is compared with other three well-known schemes. Comparative simulation results show the satisfactory estimation and control performance.