The invention discloses a flight monitoring service method and a system thereof. The method is characterized by through a black box of a low altitude flight aircraft, acquiring a position and flight path information of an unmanned aerial vehicle; after carrying out correlation processing, using an unmanned aerial vehicle air traffic control system to send peripheral flight path information of the unmanned aerial vehicle to an unmanned aerial vehicle ground control station. The system comprises a civil aviation secondary radar, a low-altitude radar, radar access equipment, mobile acquisition equipment, an ADSB ground station, mobile conversion equipment, an automatic navigator, a GPS radio station, ADSC information conversion equipment, mobile communication equipment, a Big Dipper airborne navigator, a flight monitoring cloud server and a flight monitoring information application system. The method and the system of the invention have an advantage that dynamic data of an acquired unmanned aerial vehicle flight path, a state and the like can be taken as a monitoring information source and is transmitted to an air traffic control system currently used by military and civil aviation in real time so that a management department can conveniently monitor a flight state of a low altitude airspace unmanned aerial vehicle, and a blind area of current low-altitude spatial domain monitoring is compensated.