A device for controlling a battery in a vehicle is provided and includes a sensor that senses states of charge of a plurality of batteries and a controller that controls connection of one of the plurality of batteries to adjust voltages applied to the plurality of batteries and an electronic device based on a determination result of whether a load has occurred on the electronic device connected to the one of the plurality of batteries and a state of charge of the one of the plurality of batteries. Thus, when the load occurs on the electronic device, the device controls the connection of the battery to improve a fuel efficiency.