The invention discloses an SPEG biological migration small and micro water body treatment and restoration method and system. The method comprises the following steps: S1, carrying out substrate improvement, namely, carrying out desilting-free and in-situ reduction on the substrate of a water body; S2, constructing cascade aquatic plants, namely, forming an aquatic plant community through plant optimization and cascade construction; S3, constructing a three-dimensional ecological system, namely, putting aquatic animals and aquatic plants together to form a full-ecological food chain; and S4, laying an oxygen-enriched net, namely, laying a graphene oxygen-enriched net on the surface of the water body to realize water body oxygenation and targeted degradation of pollutants through natural illumination so as to construct an oxygen-enriched clear water body. According to the invention, microorganisms, aquatic plants and aquatic animal symbiotic systems play a synergistic role to form a complete water body purification enhancement system, so that 'long-term treatment and long-term clarification' of small and micro water bodies is realized, i.e., the water quality is obviously improved, the water transparency is improved, the nutritive salt is reduced, and the establishment and recovery of water body ecology are facilitated.