The invention discloses a system and a method for cooling a vehicle-mounted charger. The cooling system comprises a wiper motor, a washing tank, a CAN/LIN bus, a charging control module, a charger radiator, an electromagnetic valve and a charger cooling pipeline, wherein the charger cooling pipeline is connected with the wiper motor and the charger radiator through the electromagnetic valve; the charger is cooled by using the washing solution in the washing tank as cooling liquid and using the wiper motor as an electric water pump; and the electromagnetic valve is connected with the water outlet of the wiper motor and is controlled by the charging control module, so that only one of a wiper water spray pipeline and the charger cooling pipeline can make the cooling liquid flow through. In the system and the method, a set of pipeline is additionally arranged on a radiating fin of the charger in a wiper system; and the rotary speed of the wiper motor is adjusted by using the charging control module according to the temperature of the charger so as to control water which flows through the radiator. The system makes full used of the existing parts of a vehicle, so the cost is low and the applicable range is wide.