The invention relates to the technical field of fire-fighting equipment, in particular to a fire extinguishing system of a perfluoro battery compartment. The fire extinguishing system comprises a fireextinguishing agent storing container, a bottle head valve I, a starting valve, a siphon, a fire extinguishing agent conveying pipeline, an agentia one-way valve, a pressure signaling device, a pipeline connecting component, a pneumatic pipeline, a gas one-way valve, a bottle head valve II, an electromagnet, a driving gas cylinder, a gas decompression machine, a pressure gage, a safe decompression device, a low-pressure sensor, an electrical circuit, a fire extinguishing system control device, a gas detector, a heat detector, a smoke detector, a UPS emergency power source, a mechanical emergency switch, an atomizer, and a box body. A fire extinguishing medium is perfluoro which is non-poisonous, colourless and with high insulation. The detectors (the gas detector, the heat detector, and the smoke detector) with high accuracy and multiple types are adopted, battery fires can be accurately and quickly detected. Automatic, manual and mechanical emergency stating modes are achieved, and therefore reliability, timeliness and accuracy of fire extinguishing system operation are guaranteed.