A system for controlling a low voltage DC-DC converter for a vehicle is provided. The system includes a low voltage DC-DC converter that converts a voltage of a main battery into a low voltage and outputs the same. An electric device is connected to an output terminal of the low voltage DC-DC converter and a first relay is connected to the output terminal of the low voltage DC-DC converter at a first terminal thereof. An auxiliary battery is connected to a second terminal of the first relay and a controller turns off the first relay and operates the low voltage DC-DC converter to output a minimum voltage capable of operating the electric device when the auxiliary battery is charged to a preset reference value or more while the main battery is being charged.