A method of treating hardly decomposable harmful substance comprising (A) a step for adding coagulant into wastewater containing a hardly decomposable harmful substance, (B) a step for performing solid-liquid separation which separates a solid containing the hardly decomposable harmful substance from a liquid, and (C) a step for decomposing the hardly decomposable harmful substance by bringing peroxide into contact with the separated solid. Efficiently and safely treating the hardly decomposable harmful substances by means of low-cost facilities realizes.