The invention provides a system and method for controlling a low-voltage DC-DC converter (LDC) voltage of a hybrid vehicle. The LDC voltage is optimally adjusted based on which driving mode the vehicle enters, thereby improving fuel efficiency. The method includes determining whether the hybrid vehicle is driven in a regenerative braking mode and whether a value of a state of charge (SOC) of an auxiliary battery is equal to or greater than a first critical value set as a value when charging of the auxiliary battery is unnecessary during the driving in the regenerative braking mode. When the value of the SOC of the auxiliary battery is equal to or greater than the predetermined first critical value, the driving mode is switched from the regenerative braking mode to an electric vehicle (EV) mode, and to variably adjust an LDC target voltage in the EV mode.