A control system for controlling a control target apparatus provided to an engine includes a main ECU and a sub-ECU. The main ECU calculates at least one operational command value according to an operational state of the engine. The at least one operational command value is used to operate the control target apparatus. The sub-ECU is independent of the main ECU, and controls the control target apparatus non-autonomously and autonomously. In non-autonomous control of the control target apparatus, the sub-ECU corrects the at least one operational command value, which is calculated by the main ECU. The sub-ECU non-autonomously controls the control target apparatus by use of the corrected at least one operational command value corrected by the sub-ECU. In autonomous control of the control target apparatus, the sub-ECU autonomously controls the control target apparatus independently of the main ECU, when a predetermined condition is satisfied.