The present invention provides a membrane separation system that makes it possible, by a process using a pervaporation membrane, to obtain a non-permeated fluid sufficiently suitable to be reused. A membrane separation system of the present invention includes a membrane separation device. The membrane separation device has a pervaporation membrane. The pervaporation membrane separates a fermented liquid containing a volatile organic compound and a microorganism that generates the organic compound into a permeated fluid and a non-permeated fluid. The membrane separation system adjusts a temperature of the membrane separation device so that an absolute value of a difference between a temperature T1 ( C) of the fermented liquid to be supplied to the membrane separation device and a temperature T2 ( C.) of the non-permeated fluid discharged from the membrane separation device is less than 10 C.