A battery control system includes a main battery and an auxiliary battery, a direct current DC-DC converter for converting a high voltage output from the main battery into a low voltage between the main battery and the auxiliary battery and supplying the converted low voltage to the auxiliary battery or an electronic load, a relay for intermitting a voltage of the auxiliary battery, and a battery management system for controlling the relay to be turned off in a state in which the DC-DC converter is operated in a constantly ON state, comparing an output voltage of the DC-DC converter and a summation of cell voltages of the auxiliary battery, and detecting a fusion state of the relay according to a comparison result.