A vehicle battery controlling apparatus is provided and includes a sensor that senses a SOC of a battery connected to a switch among a plurality of batteries and a controller that controls the on/off of the switch based on a first result of determining whether a vehicle enters a fuel-cut section and a second result of comparing the SOC of the battery with at least one or more predetermined reference values. The apparatus improves fuel efficiency by increasing energy regeneration, and improves battery durability by minimizing battery SOC in a non-regeneration section.