A variable air intake control system includes first and second variable intake control valves, a vacuum tank, actuators, a one-way valve and a controller. The controller selectively is configured to control the first and second actuators to offset operating timings of the first and second variable intake control valves so as to suppress the noise in the one-way valve, when the first and second variable intake control valves are switched from a first operating state in which the first and second variable intake control valves are both in one of the open and closed states to a second operating state in which the first and second variable intake control valves are both in one of the open and closed states that is opposite to the first operating state.