The invention provides a shallow-water three-dimensional multi-layer intensive high-density aquaculture system which comprises multiple layers of shallow-water aquaculture tanks arranged up and down, a water injection pipeline, double-layer drainage pipes and water treatment integrated equipment, wherein the water injection pipeline is arranged above the shallow-water aquaculture tank on the uppermost layer and used for controlling the water injection amount; a water inlet and a water outlet of each layer of shallow-water aquaculture tank are located in the diagonal direction of the aquaculture tank, and one double-layer drainage pipe is arranged in each layer of shallow-water aquaculture tank; and the lowest layer of shallow-water aquaculture tank is connected with the water treatment integrated equipment, and the water treatment integrated equipment is used for purifying sewage discharged from the upper part. By adopting a self-circulation drainage mode from top to bottom, combining devices such as the double-layer drainage pipes, an unpowered dissolved oxygen supercharger and a residue separator and cooperating with water treatment integrated equipment, the water dissolved oxygen amount can be increased, the water quality can be improved, diseases can be reduced, effects of no emission, no pollution, no chemical and no antibiotic can be achieved, and the formed product is green, safe, ecological and environmentally friendly.