An aircraft control system includes a target instruction value calculation unit acquires a target instruction value to set an aircraft in a target state, a reference velocity calculation unit inputs, to a reference model in which reference velocity corresponding to a reference value of aircraft velocity is set uniquely as an output value according to an input value, a value based on the target instruction value as the input value. A relative velocity calculation unit calculates relative velocity of the aircraft to a target position, the relative velocity being used in control of the aircraft. An estimated disturbance quantity calculation unit calculates an estimated disturbance quantity acting on the aircraft, based on a difference between the relative velocity and the reference velocity, and a correction target instruction value calculation unit corrects the target instruction value, based on the estimated disturbance quantity calculated at a previous timing.