The invention relates to a continuous flow three-section biological electrogenesis desalination device for treating acetonitrile-containing refining waste water and an application method thereof, belonging to the field of the refining waste water treatment, and aiming at solving the problem that the resource is wasted in the existing chemical industrial waste water treatment process. The continuous flow three-section biological electrogenesis desalination device comprises an anode chamber, an anode carbon brush, an anion exchange membrane, a desalination chamber, a cation exchange membrane, a cathode carbon brush, a cathode chamber, a reference electrode, an aeration device, a facultative chamber, a resistor and a water pump. The application method comprises the following steps: generating an anaerobic electrogenesis biological membrane, an aerobic electrogenesis biological membrane and facultative anaerobic active sludge by virtue of culturing and acclimatization; and facilitating the flow of the water to be treated in various treatment chambers in a gravity flow manner, thereby obtaining stable electric energy output. A continuous running way is adopted to treat the waste water so as to degrade the organic matters and efficiently remove the salt, so that the treatment to toxic and harmful substances is realized, the stable electric energy output can be obtained, no additional energy input or high penetration pressure is needed in the continuous flow three-section biological electrogenesis running process, and the application prospect is good.