The present invention discloses an on-line cleaning control system and method for carbon deposits in a direct injection engine fuel system. The system comprises a cleaner tank, a cleaner input pipeline, an electromagnetic flow controller and a control circuit. A liquid transfer pump is in series connection with a pipeline of the cleaner input pipeline and the cleaner tank; when the conditions that fuel is injected through a fuel injector of the engine, the temperature of a three-way catalytic converter is lower than 800° C., the rotational speed of the engine is greater than 1200 rpm and the cleaning time is shorter than set cleaning time are met, the control circuit starts a cleaning working procedure to inject a cleaner into an intake manifold of the engine. According to the present invention, the liquid transfer pump is used for actively injecting the cleaner into an intake valve of the engine, and besides, the optimal cleaning condition of the engine is controlled; a starting switch can be arranged in a cab so that on-line cleaning for the carbon deposits in the intake valve and a combustion chamber of the engine is performed actively according to the usage state of an automobile; and also, by receiving a mileage signal and presetting a mileage starting value in the controller, on-line cleaning for the carbon deposits in the intake valve and the combustion chamber of the engine can be performed automatically and periodically in accordance with mileages.