Disclosed is a method of controlling an air supply system for a fuel cell. The air supply system includes a fuel cell stack, an air channel to supply air to an inlet of the fuel cell stack, a gas adsorption unit disposed on the air channel and configured to adsorb oxygen contained in air introduced into the air channel. In particular, the method includes: determining whether a power generation operation of the fuel cell stack is resumed; when the power generation operation of the fuel cell stack is resumed, controlling a voltage source to apply a voltage to the gas adsorption unit; and supplying air to the fuel cell stack through the air channel in a state in which the voltage is applied to the gas adsorption unit.