A membrane separation device includes a separation membrane immersed in water to be treated and an air diffusion device positioned below the separation membrane, and provides treated water that has permeated through the separation membrane while diffusing air from the air diffusion device towards the separation membrane. A target value setting step sets a target value of an amount of diffusion air diffused from the air diffusion device based on a transmembrane pressure difference, and the air diffusion device is controlled such that the amount of the diffusion air becomes the target value. In the target value setting step, an absolute value of a change or a rate of change in the target value for increasing the amount of the air diffusion is set greater than an absolute value of a change or a rate of change in the target value for decreasing the amount of the air diffusion.