For linear multiple input multiple output (MIMO) systems with mismatched parameter uncertainties and matched nonlinear perturbations, a compensator‐based controller based on the disturbance estimation algorithm is considered in this paper. We design a reduced‐order high‐gain observer to estimate the effect of matched perturbation, and introduce the estimation information into the controller design. Using singular perturbation theory, the proposed control law can guarantee robust stability of the closed‐loop system. Moreover, the peaking phenomenon in the control input during the transient time can be effectively avoided using our method. Finally, the feasibility of the proposed method is illustrated by a numerical example.