The present invention provides a method for controlling a charging voltage of a 12V auxiliary battery for a hybrid vehicle, which can (1) improve charging efficiency of an auxiliary battery by increasing the output voltage of a DC-DC converter during cold start when the outside air temperature is low, (2) improve the charging efficiency of the auxiliary battery by increasing or decreasing the output power of the DC-DC converter according to the state of charge of the auxiliary battery and by increasing the output voltage of the DC-DC converter when many electrical loads are turned on, and (3) allow the DC-DC converter to provide continuous power supply for charging the auxiliary battery by turning on a main switch disposed between a high voltage battery and the DC-DC converter based on a reverse power conversion operation of the DC-DC converter even in the case where the voltage of the auxiliary battery falls below 9V.