A control device, which is applied to an in-vehicle internal combustion engine equipped with an intake valve variable timing mechanism that varies the valve timing for an intake valve, and which intermittently operates the in-vehicle internal combustion engine by automatically stopping/restarting the engine, wherein the electronic control unit does not permit the engine operation to be automatically stopped when the intake valve variable timing mechanism malfunctions at an operating position closer to the advanced angle than the operating position for the most retarded angle of the variable range for the valve timing of intake valve, and thus preventing increased engine vibration and misfires when the engine automatically restarts, which are caused by a malfunction of the variable valve mechanism.