A synergistic effect between strong electron correlation and spin–orbit interaction has been theoretically predicted to realize new topological states of quantum matter on Kondo insulators (KIs), so-called topological Kondo insulators (TKIs). One TKI candidate has been experimentally observed on the KI SmB6(001), and the origin of the surface states (SS) and the topological order of SmB6 has been actively discussed. Here, we show a metallic SS on the clean surface of another TKI candidate YbB12(001) using angle-resolved photoelectron spectroscopy. The SS shows temperature-dependent reconstruction corresponding to the Kondo effect observed for bulk states. Despite the low-temperature insulating bulk, the reconstructed SS with c–f hybridization is metallic, forming a closed Fermi contour surrounding on the surface Brillouin zone and agreeing with the theoretically expected behaviour for SS on TKIs. These results demonstrate the temperature-dependent holistic reconstruction of two-dimensional states localized on KIs surface driven by the Kondo effect.