According to one embodiment, a membrane filtration system includes a raw water tank, a pretreatment membrane module, a raw water feed line, a high-pressure RO membrane module, a high-pressure line, a preceding power recovery unit which pressurize the pretreated water by transmitting the pressure of the concentrate to the pretreated water, a succeeding power recovery unit which pressurize the raw water by transmitting a remaining pressure of the concentrate to the raw water, a concentrate discharge line, a first pressure transmission line communicating to the power recovery unit by being branched from the high-pressure line, a second pressure transmission line communicating to the power recovery unit by being branched from the raw water feed line, and a valve provided in the drain line to regulate a discharge of the concentrate from the power recovery unit in accordance with a pressure loss in the pretreatment membrane module.