The present invention membrane filtration water treatment system, and relates to its operation method, placing the pressure-precision filtration membrane module, a nanofiltration membrane module and a submerged microfiltration membrane module, and re-use can be concentrated and automatically control it to the constant production with a high recovery rate It will increase the recovery rate to drop the production cost per ton, as well as reduce the operating costs of the membrane filtration water treatment system and its operation method which can secure the advantage compared to conventional processes that require less land area required by.