A method and system are provided for variably adjusted voltage of the LDC applied with an IBS (Intelligent Battery Sensor). The LDC output voltage control mode is determined in each of three driving modes, and the high electric loads are separated into two or more groups. The LDC output voltage value and the order priority are differentiated based on the durability of the auxiliary battery. Additionally, an LDC output voltage order table is generated according to the driving mode and the SOC state based on the auxiliary battery SOC information obtained from an IBS. Thus, consumed energy of the LDC and an energy consumption amount of the auxiliary battery are minimized, thus improving fuel efficiency.