A system and method for controlling a vehicle thermal management apparatus, may include a component state unit of collecting a state of a vehicle component, a disturbance collection unit of collecting a state of a disturbance affecting thermal management of the vehicle component, a determination unit of calculating an amount of heat exchange between the vehicle component and a thermal management apparatus, which is required in the future, based on a past state value of the vehicle component collected through the component state unit and a past state value of the disturbance collected through the disturbance collection unit, and an operation unit of controlling operation of the thermal management apparatus based on the amount of heat exchange determined by the calculation unit.