A system and a method for controlling a low voltage DC/DC converter (LDC) of a hybrid vehicle is provided in which a fuel efficiency mode for artificially turning off pulse width modulation (PWM) control of the LDC is added, thereby improving fuel efficiency. Accordingly, the fuel efficiency mode for artificially turning off the PWM control of the LDC is added, so that when the fuel efficiency mode is performed, power of an auxiliary battery is temporarily supplied to an electric field load, thereby reducing power consumption of a main battery and improving fuel efficiency. Further, when the auxiliary battery is separated, power of the main battery is temporarily supplied to the electric field load by performing the PWM control of the LDC, to prevent a phenomenon that power is not supplied to the electric field load when the auxiliary battery is separated.