A method of treating a wastewater, containing the steps of: filtering a wastewater supplied into an activated sludge tank and biologically-treated therein, in a membrane module installed outside the activated sludge tank; chemical-cleaning the membrane module with a membrane-cleaning agent while the membrane module is disconnected from the activated sludge tank with a valve; and water-flushing off the substances contained in the wastewater that react with the membrane-cleaning agent and form hazardous substances and/or operation-inhibiting substances, or the membrane-cleaning agent remaining in the membrane module with water while the membrane module and the activated sludge tank are disconnected from each other by the valve, wherein the membrane-cleaning agent is prevented from contacting the substances contained in the wastewater that react with the membrane-cleaning agent and form hazardous substances and/or operation-inhibiting substances.