In this article, we study the output tracking control of a class of MIMO nonlinear non-minimum phase systems in the presence of input disturbances. In order to attenuate the effects of disturbances, the method of uncertainty and disturbance estimator (UDE) is extended to the controller design for non-minimum phase systems. Due to the fact that the accumulated disturbances is composed of internal states and external disturbances, a different stability analysis is given, and the overall closed-loop system is proved to be semi-globally stable. The proposed state-feedback controller not only forces system outputs to asymptotically track desired trajectories, but also drives the unstable internal dynamics to follow bounded and causal ideal internal dynamics (IID) solved via stable system centre (SSC) method. Simulation results demonstrate that the proposed controller achieves excellent tracking and disturbance rejection performance via the example of VTOL aircraft which has been the benchmark of nonlinear non-minimum phase systems.