The electropolishing (EP) mechanism of niobium (Nb) in relatively eco-friendly deep eutectic solvents (DES) instead of the widely used HF-based electrolyte was studied by anodic polarization (AP) tests and electrochemical impedance spectroscopy (EIS) using a rotating disk electrode (RDE) of Nb. The AP test results reveal that the EP progress of Nb is under a mixed control of ionic transport and charge transfer. EIS results suggest the niobium EP process is consistent with the compact salt film mechanism in this electrolyte. The influence of applied potential and electrolyte temperature on the EP rate, surface roughness, and surface glossiness of Nb was also investigated. The crystal structure, chemical composition and surface morphology of Nb samples before and after EP were analyzed by XRD, XPS, and SEM. The grain sizes and preferential orientation of Nb before and after EP are changed. XPS depth profiling has been produced by sputtering with Ar+ ions which revealed that with the increase of Ar+ sputtering depth, the content of low-valence Nb0, NbO increases, high-valence Nb2O5 decreases, and middle-valence NbO2 increases first and then decreases. It indicates the existence of the Nb → Nb2+→Nb4+→Nb5+ transition process. An even and mirror-like Nb surface can be obtained after EP from DES.