Thanks to the high specific surface area and low tortuosity for ionic storage and transportation, holey graphene has been regarded as a promising material for energy storage devices such as lithium ion batteries and supercapacitors. For practical application, a scalable and green preparation method for holey graphene is required. This work proposes a facile preparation method of holey graphene just by microwaving pristine graphene in air. Compared with previous scalable methods, this method exhibits much higher efficiency to reduce the preparation time from hours to minutes. The mechanism underlying the microwave irradiation-induced formation of nanosized holes involves the interaction among microwave, electrons, oxygen in air, and carbon atoms in defect area of graphene. The size, density and distribution of holes can be controlled by tuning microwave irradiation time and oxygen concentration. Used as hybrid conductive agent, the as-prepared holey multilayer graphene improves capacitance retention to 96.25% at high current density (8 A/g) and 96.48 % in long cycles (1 A/g and 10000 cycles).