Natural sponge is an ancient marine organism with a single lamellar structure, on which there are abundant porous channels to compose full-fledged spatial veins. Illumined by the natural spongy system, herein, the Cl doped surface defective graphite carbon nitride (g-C3N4−xClx) was constructed through microwave etching. In this process, microwave with HCl was employed to produce surface defects and peel bulk g-C3N4 to form natural spongy structured g-C3N4−xClx with three-dimensional networks. The spongy structure of the photocatalyst could provide abundant and unobstructed pathways for the transfer and separation of electron–hole pairs, and it was beneficial for photocatalytic reaction. The spongy defective g-C3N4−xClx achieved excellent degradation of diclofenac sodium (100%), bisphenol A (88.2%), phenol (85.7%) and methylene blue (97%) solution under simulated solar irradiation, respectively. The chlorine atoms were introduced into the g-C3N4 skeleton in microwave field with HCl, forming C–Cl bonds and surface polarization field, which could significantly accelerate the separation of photogenerated electrons and holes. As an efficient and universal approach, microwave etching can be generally used to create surface defects for most photocatalysts, which may have potential applications in environmental purification, energy conversion and photodynamic therapy.