The beam energy measurement system (BEMS) at the upgraded Beijing Electron-Positron Collider (BEPCII) is designed to provide beam energy value with the relative error at the level of 5×10−5. The obvious energy deviation found during J/ψ resonance scan in 2012 leads to great amount of investigations on both BEPCII and BEMS sides. The reasons causing such an unexpected difference are figured out, which include the neutron damage to HPGe detector, the leakage of RF cavity, and the background from Linac. Based on a series of measures, the ψ(3686) line shape scan is designed and performed, the experimental result indicates that BEMS can measure the beam energy with the claimed accuracy. The afterward performance of BEMS is smooth and stable, and BEMS will play a crucial role in the following high accurate experiments.