This paper presents an improved model predictive control (MPC) algorithm for linear systems with input disturbance. Based on the developed extended non-minimum state space input disturbance (ENMSS-ID) model, the input disturbance model structure is incorporated into the MPC framework and the objective function of the MPC optimization problem is improved to weigh the system output increments. This enables the algorithm simultaneously to achieve good input disturbance rejection performance for systems with known input disturbances and reduce the controllers’ sensitivity to model mismatch. An existing optimal estimation method is introduced to estimate the input disturbance, together with the proposed strategy to improve estimation convergence. Offset-free property is also proven to show the steady-state performance of the designed control scheme. Finally, two benchmark plants are studied to illustrate the effectiveness and advantages of the proposed algorithm.