The pre-alignment units of the High Energy Photon Source (HEPS) are numerious and require extremely high precision in magnet alignment. To verify the magnetic alignment accuracy of the pre-alignment magnet unit in the HEPS booster, vibration wire magnetic center verification measurements need to be carried out in the experimental hall at a certain ratio. Based on the vibration wire system developed in the pre-research stage, a detailed study is conducted to introduce the measurement principle and scanning method of the vibration wire magnetic center. The research focuses on the magnetic center allignment accuracy detection method of the two magnet units in the HEPS booster and conducts verification experiments. A high-precision repeat positioning clamping mechanism for the vibration wire was designed and constructed, and a method for correcting the sag of the vibration wire was studied. The magnetic center scan results of the two magnet units in the booster were analyzed by fitting. The experimental results show that the pre-alignment accuracy requirement of the HEPS booster for a relative position error between magnets better than 50 μm is satisfied. This study provides a reference for accurate measurement of the vibration wire magnetic center in other accelerator pre-allignment magnet units.