The invention relates to a system for ecologically treating aquaculture wastewater, which comprises a primary storage pool, an accident pool, a solid-liquid separation zone, an earthworm composting zone, a regulation sedimentation pool, an anoxic pool, a gas collection system, an OAO system, a secondary sedimentation pool, an artificial natural layer filter pool and an impounding reservoir. The system has the advantages of 1, low investment cost, low operation cost, less quantity of energy-consuming members; 2, simple process, convenience for implementation, good generality, capability of adapting to the treatment of the aquaculture wastewater of different aquaculture occasions and aquaculture cells; 3, high treatment efficiency and capability of enabling effluent to reach the requirementof emission when the standard is met; 4, simpleness in maintenance, periodic spoil disposal, periodical inspection, no need of operation of specially-assigned person; 5, capability of generating a certain economic benefit while the aquaculture wastewater is treated; 6, high environment protection degree because rice and wheat straws, coconut shells and tree barks, which are discarded in countries, are recycled; and 7, a certain landscape value, wherein valuable products include an organic fertilizer, earthworms and methane; and grasses, trees and vegetations which are enjoyed by people can beplanted.