Actively tuning thermal transport properties of materials at nanoscale is of great interest in many applications. In this work, we demonstrated reversible copper (Cu) intercalation on individual bismuth selenide (Bi2Se3) nanoribbons and investigated the effects of intercalation/de-intercalation of Cu atoms on their thermal transport properties. Distinct from prior studies that have shown reduced thermal conductivity (κtot) after intercalation, a crossover in κtot was observed over the measured temperature range in this work, i.e., κtot is significantly suppressed at low temperatures but enhanced above 250 K by Cu intercalation. This intriguing crossover phenomenon is attributed to the interplay between the enhanced electronic thermal conductivity (κe) and the reduced lattice thermal conductivity (κph), both of which result from the intercalated Cu atoms. Moreover, we showed that thermal conductivity could be further tuned by the de-intercalation of Cu atoms. Compared to the pristine nanoribbon, a dramatically lower in-plane κph was observed for intercalated and de-intercalated nanoribbons due to the formation of the Cu/Bi2Se3 superlattice structure. Theoretical modeling revealed that the reduced κph was primarily owing to the enhancement of phonon boundary scattering and point defect scattering. This work provides a facile approach to tune thermal transport properties at nanoscale, which can be potentially used in thermal switch and thermoelectric applications.