Disclosed are method and apparatus for controlling the supply of power in an electronic device are provided. The apparatus includes two or more batteries, a mutual charging prevention controller, a sequential discharging controller, and a controller that detects remaining capacities of the two or more batteries, charges a main battery of the two or more batteries in a single charging mode, when the remaining battery capacity of the main battery is less than or equal to a preset remaining battery capacity set to select a charging mode, and simultaneously charges the two or more batteries, when the remaining battery capacity of the main battery is greater than the preset remaining battery capacity.