Magnetron sputtering is an alternative approach to prepare flexible copper clad laminates because of low cost and thin copper clad laminate thickness. However, Cu film has poor adhesion when directly deposited on polymer substrates, imposing certain limits to the use of magnetron sputtering technique. In this work, Cu film was deposited on polymer substrates including polyimide, polyethylene terephthalate and polytetrafluoroethylene. Different metal interlayers were introduced into the polymer/Cu interfaces to improve the adhesion between polymer substrates and Cu film. It was found that the metal interlayer could significantly improve the adhesion strength of Cu film to polymers and a reasonably rough polymer surface could also enhance the mechanical bonding with Cu film. A metal Ni interlayer provides the best adhesion enhancement, which is associated with the same crystal structure between Ni and Cu as well as their excellent solid solubility. Meanwhile, a metal interlayer also contributes to Cu (111) orientation growing during deposition. This proposes a promising route to overcome the wear adhesion problem between Cu film and polymers in the preparation of magnetron sputtered flexible copper clad laminates.