Advanced treatment method and system of ethanolamine-containing wastewater are disclosed, which perform physicochemical and biological treatment processes. The method regenerates cation exchange resin that captures ethanolamine discharged from a nuclear power plant or a thermal power station, concentrates the ethanolamine-containing wastewater to reduce the volume of the wastewater, and then treats the highly concentrated ethanolamine-containing wastewater through biological decomposition and denitrification processes. The system for treating ethanolamine-containing wastewater performs the physicochemical process (ion-exchange and resin regenerations) where the waster is concentrated, and then applies the biological process to the small amount of wastewater highly concentrated. The physicochemical process is composed of exchanging ions and eluting/concentrating ethanolamine using sodium hydroxide. The wastewater of a few to tens of thousands ppm is transferred and undergoes a biological process where the ethanolamine is decomposed, converted into CO.sub.2 and N.sub.2 through the anoxic tank and two aerobic tanks, and then discharged in gas. Therefore, the wastewater is discharged, satisfying the biochemical oxygen demand value and the nitrogen content required by the environmental discharge standard.