The invention, which relates to the unmanned aerial vehicle field, discloses an unmanned aerial vehicle flight control system based on electromagnetic field ranging and a working method thereof. During the existing unmanned aerial vehicle flight process, the distance to a power transmission line is usually judged by the naked eyes and thus the requirement on the worker is high; and the collision with a power transmission line by an unmanned aerial vehicle in inspection occurs frequently. According to the invention, the unmanned aerial vehicle flight control system comprises an electromagneticfield measuring module, a flying height measuring module, a data processing module, a safety control module and a flight control module. The electromagnetic field measuring module measures an electromagnetic field component of the flying position in real time; the flying height measuring module measures the flying height of the unmanned aerial vehicle in real time; the data processing module calculates change rates of electric field and magnetic field components of the flying position and corresponding dangerous thresholds in real time; the safety control module determines and monitors the flying state of the unmanned aerial vehicle in real time; and the flight control module controls the unmanned aerial vehicle to fly. Therefore, the safety of the inspection of the unmanned aerial vehicleis improved; the inspection cost of the transmission line is lowered; and the high reliability and safety of the transmission line operation are ensured.