The invention provides an anchor point identifying system and method based on a total station. The system comprises an air vehicle, a prism, a point target locking device, a PC terminal and the total station; the prism is located on the upper portion of the air vehicle, the point target locking device is located on the lower portion of the center of the air vehicle, and the PC terminal is in parallel control connection with a single chip microcomputer of the six-rotor-wing air vehicle, so that the air vehicle arrives at the specified coordinate position and is calibrated. Compared with a traditional method, traditional manual calculation is replaced with the method that the total station is adopted to cooperate with the air vehicle to carry the prism to determine coordinates, and therefore errors brought by site situations can be reduced; meanwhile, anchor point identifying is conducted through the six-rotor-wing air vehicle, therefore, tediousness of manual measurement is avoided, the rugged road condition on a working platform is avoided through low-altitude flying, and anchor point identifying is more accurate, easier, faster, more efficient and more convenient.