This paper investigates the disturbance observer based robust cruise control problem for the heavy haul train with input saturation and disturbances. Both uncertain parameters and actuator saturation are taken into account in the dynamic model of the heavy haul train. To reject the influence of disturbances from the input channel, a linear disturbance observer is proposed to approximate the unknown disturbance, and an augmented system is constructed by combining the train state and the disturbance estimation error. According to the Lyapunov stability analysis method and the guaranteed cost control theory, a sufficient condition for the existence of the composite state-feedback control law and the disturbance observer parameter matrix are obtained, the coupler deviation and the disturbance estimation error are stable at the equilibrium point, and meanwhile the minimization of a given train performance index is ensured. Numerical experiments are provided to illustrate the effectiveness of the proposed approach.