In regard to the nonminimum phase MIMO discrete time systems, a method using estimation method in designing an observer-based output tracking controller is proposed in this paper. Provided the variation of the disturbance in the two consecutive sampling instances is not changed significantly, both the system state and the unknown disturbance can be simultaneously estimated by our proposed observer algorithm with the estimation error being constrained in a small bounded region of the order of O ( T ). The control law including a feedforward term and a feedback input can cause the tracking error to be bounded in a small region with the guarantied system stability. A numerical example is presented to demonstrate the applicability of the proposed control scheme.