To meet the requirements of rotor axial center trajectory measurement in helicopter flight state, an axial center trajectory measurement method based on low-altitude binocular vision was proposed. Firstly, for the small-value measurement of high-speed rotating objects, based on the principle of stereo vision measurement, a visual measurement system of rotor axial center trajectory with unmanned aerial vehicle (UAV) as a low-altitude mobile platform was designed and constructed. Secondly, according to the environmental conditions of dynamic measurement, a measurement system calibration method combining ground calibration and aerial dynamic real-time calibration was proposed. Then, based on the spatial geometric relationship, the static estimation and dynamic trajectory measurement methods of rotor axial center were discussed. Finally, the ground accuracy verification test of the measurement system and the rotor axial center trajectory measurement test of the helicopter ground start-up state were carried out. Experimental results show that the method is accurate and reliable, and the distance accuracy between points is better than 1‰, which can realize the non-contact accurate measurement of the axial center trajectory, and can also be applied to other dynamic small-value measurement tasks.