The invention discloses a stereoscopic ecological elimination system for endogenous pollution of water bodies. The stereoscopic ecological elimination system is arranged in the water bodies and comprises a benthic animal enclosure and an endogenous pollutant treatment device, wherein the benthic animal enclosure comprises a rectangular pipe partially buried on bottom sediments of the water bodies;an upper surface of the rectangular pipe is not sealed; benthic animals having disturbance capability are put into the benthic animal enclosure; the endogenous pollutant treatment device comprises afixed part and a filler medium carrying microorganisms; the filler medium is fixed on the fixed part; and the endogenous pollutant treatment device is located in an upper space of a downstream of thebenthic animal enclosure. According to the stereoscopic ecological elimination system provided by the invention, integrity of the ecosystem is fully considered, endogenous pollutants are removed without damaging the bottom sediments of rivers or lakes and the ecosystem, simultaneously, a degradation process of pollutants is considered, and the endogenous pollutions are gradually and fundamentallyeliminated; by adopting the biotechnology used in the invention, costs are saved, the engineering operation is simple and the operation amount is small.