A method for controlling a plurality of batteries and an electronic device thereof are provided. The electronic device includes a power management circuit configured to supply power to the electronic device; a first battery electrically connected with a power input port of the power management circuit; a second battery electrically connected with the power input port; a first charging circuit configured to charge the first battery; a second charging circuit configured to charge the second battery; a first current control circuit electrically connected between the first charging circuit and the first battery, and configured to control a first charging current supplied from the first charging circuit to the first battery and a leakage current due to a voltage difference between the first battery and the second battery; and a second current control circuit electrically connected between the second charging circuit and the second battery, and configured to control a second charging current supplied from the second charging circuit to the second battery and the leakage current.