Abstract: With the rapid development of flexible electronics, wearable devices, high-frequency communications, and the aerospace industry, there is a growing demand for flexible copper-clad laminates that combine lightweight construction, high flexibility, and excellent electrical performance. The use of vacuum deposition technology to metallize the surface of ultra-thin polyimide films is a major current trend. However, due to the high chemical inertness and poor wettability of polyimide, it is difficult to achieve a highly reliable bond with the metal layer, which limits the application of this technology in ultra-thin, adhesive-free, two-layer flexible copper-clad laminates. At this stage, high-energy ion implantation is regarded as a key pretreatment method for enhancing the adhesion strength between the film and the substrate, as it can induce physicochemical changes on the surface of the polymer, such as bond breaking, cross-linking, carbonization, and the generation of active groups, thereby effectively improving surface activity and forming a functional transition layer. Based on this, this study utilized MEVVA ion implantation technology to create a highly reactive interface on the surface of a 25 μm thick polyimide film, followed by the deposition of a copper coating via DC magnetron sputtering. By analyzing the effects of different ion implantation energies on the microstructural properties of PI films and copper layers, including surface morphology, chemical composition, and surface characteristics, as well as macroscopic properties such as the electrical performance of the copper layer and the film-substrate bond strength, the study on the mechanisms by which ion implantation influences surface metallization was completed. The results indicate that as the incident energy increases, the macromolecular chains in the PI film undergo fragmentation and reorganization, leading to a linear decrease in surface roughness; consequently, the grain size and intergranular spacing of the copper film deposited on this substrate gradually decrease. When the implantation energy is 40 keV, the coating exhibits a sheet resistance of 36 mΩ/sq and a bond strength of 5.81 MPa, demonstrating optimal electrical and mechanical properties. This indicates that the macroscopic comprehensive performance of the copper film is jointly governed by multiple factors, including grain structure, impurity distribution, defect density, and stress state. In summary, the use of metal ion implantation within an appropriate energy range as a pretreatment process can significantly improve the electrical properties and film-substrate adhesion strength of flexible copper-clad laminates, providing a viable approach for the industrial production of ultra-thin, adhesive-free, two-layer flexible copper-clad laminates. Through precise interface control, the deep integration of ion implantation and vacuum deposition technologies is expected to lead to the development of new, highly reliable fabrication techniques for flexible devices.