An apparatus of preventing over-discharge of a battery for a vehicle includes a voltage sensor for sensing a voltage of the battery, a relay for preventing the over-discharge of the battery, a power state sensor for sensing an ignition on state, and a controller for outputting a warning message when the voltage of the battery becomes a first threshold value in the ignition on state and for turning off the relay after transmitting shut-off commands to the respective electronic control units (ECUs) through a vehicle network when the voltage of the battery becomes a second threshold value.