A method for treating ship ballast water with a membrane, which can easily separate and reliably remove a fouling substance attached to a membrane and maintain the membrane flux for long periods.The method including a membrane separation step of taking in seawater in a port area in which a ship is anchored and separating a microorganism with a size equal to or greater than a predetermined size therefrom with a membrane filtration apparatus installed in or on a hull of the ship and having a filtration membrane module, a backwash step of separating a fouling substance attached to a membrane surface of the membrane filtration apparatus from the membrane surface by backwashing is provided.