The invention discloses an unmanned aerial vehicle-mounted lofting system for high-speed railway piers and a lofting method thereof. The unmanned aerial vehicle-mounted lofting system comprises a ground control station, a measurement unit, an unmanned aerial vehicle and a lofting tooling; a prism and a lofting point marking device are arranged on the lofting tooling; and a vehicle-mounted controller of the lofting tooling, a load module and a flight control navigation module of the unmanned aerial vehicle, and the measurement unit are all wirelessly and communicably connected with the ground control station. According to the system and the method, the unmanned aerial vehicle is adopted to remotely control the lofting, so that the labor force and lofting difficulty of the lofting personnelare greatly reduced, the lofting correctness is high, and the high-speed railway pier construction quality is ensured.