A method of controlling a low voltage DC-DC converter of a hybrid vehicle includes determining whether cold cranking of the hybrid vehicle occurs based on a size and a rate of change of a detection value obtained by detecting a voltage of the auxiliary battery, a first adjusting operation of setting an output voltage command of the low voltage DC-DC converter to substantially the same value as the detection value and adjusting an output voltage of the low voltage DC-DC converter when determining that cold cranking occurs in the determining, and a second adjusting operation of adjusting the output voltage command and adjusting an output voltage of the low voltage DC-DC converter based on whether the detection value is increased or reduced and a comparison result between the detection value and a size of the output voltage command.