A method and apparatus for controlling power of a Base Station (BS) in a wireless communication system are provided, in which a voltage comparator compares an operation voltage of a power control target of the BS with a minimum required voltage for the power control target, and a controller decreases the operation voltage of the power control target by a predefined level, if the operation voltage is higher than the minimum required voltage, and increases the operation voltage of the power control target by a predefined level, if the operation voltage is lower than the minimum required voltage.