A method for controlling a grid-connected power supply system having multiple power supply modules, a relay commonly connected to output terminals of the power supply modules and connected between the power supply modules and a mains power grid, and a controller controlling each power supply module and the relay. The method is performed by the controller after the grid-connected power supply system is started and has steps of determining if each power supply module outputs power, activating each power supply module and charging an energy storage capacitor of the power supply module, and activating the relay when the stored voltages of the energy storage capacitors of all the power supply modules are greater than a preset peak voltage of the mains power. Accordingly, required number of relays is reduced and the size of the system can thus be more compact.