A flight control system for an unmanned aerial vehicle comprises an unmanned aerial vehicle on which a reflector is mounted and a total station for tracking the reflector and for acquiring measurement data including three-dimensional coordinates of the reflector, wherein the total station comprises a tracking module for tracking the reflector, a data transmitting module having an optical axis parallel or approximately parallel to a tracking optical axis of the tracking module and for emitting a data transmitting light, and a TS-arithmetic control module, wherein the unmanned aerial vehicle has a photodetector for receiving the data transmitting light and for emitting a photodetecting signal and a UAV-arithmetic control module for controlling a flight of the unmanned aerial vehicle, and wherein the TS-arithmetic control module is configured to superimpose the measurement data on the data transmitting light, and the UAV-arithmetic control module is configured to separate the measurement data from the photodetecting signal and obtains a flight position of the unmanned aerial vehicle in real time.