To provide a method for cleaning a separation membrane capable of cleaning the separation membrane while preventing an operating rate and a water recovering rate of a membrane filtering installation from lowering.

The method for cleaning the separation membrane 2 filtering with the membrane an in-tank water drawn from a biological treatment tank 1 to the outside by a cross-flow way comprises carrying out a plurality of times a pulse back cleaning which is accomplished by applying a back pressure to a primary side from a secondary side of the membrane between the events of the regular back cleaning. The pulse back cleaning is carried out under the condition that the pressure difference of the separation membrane is not greater than 80% of an allowable pressure difference of the membrane, wherein a deposited matter on the surface of the membrane is peeled off and returned to the biological treatment tank on a circulation flow. The regular back cleaning removes a clogging matter of the separation membrane in the opposite direction to the pulse cleaning by setting a discharging side of a back cleaning discharging water to a inlet side of the separation membrane.

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