Due to the advantages of lightweight, flexibility and high wiring density, flexible copper clad laminate (FCCL) provides a strategy for realizing the flexibility of microelectronic products. However, the widely used three-layer flexible copper clad laminate (3L-FCCL) has many drawbacks, such as micro defects, poor adhesion, poor thermal stability and high-speed signal loss, which can not meet the development trend of high integration, high density and high frequency in the field of microelectronics. In this work, the gradient metallization structure was fabricated on the surface of flexible polyimide based on energetic ion beam technology, which provided a solution for the preparation of ultra-thin flexible copper clad laminate. The Ni+ ion implantation introduced a lot of defects on the surface of polyimide, the roughness increased from 1.33 nm to 2.14 nm, and needle-like microstructure could be detected. XPS and ATR-FTIR spectra indicated that the extensive fracture of the carbonyl (C==O) and the imide (C—N) in PMDA was accompanied by the formation of the Ni—O and Ni—N complex during the process of Ni+ ion implantation. The reaction molecular dynamics (ReaxFF-MD) simulation indicated that the energy transfer caused by elastic collision was far greater than the fracture energies of carbonyl (C==O), imide (C—N) and C—H bond, which resulted in the extensive fracture of these corresponding chemical bonds. These separated N, O and H atoms became free atoms with certain kinetic energies. Subsequently, these free atoms moved to the vicinity of free radicals and formed amine (—NHR) and amide (—NHCOR) groups. In addition, it was observed that the incident Ni+ ions chelated with the carbonyl (C==O) and the imide (C—N) in PMDA and formed the new Ni—N and Ni—O chelates. Due to the cascade effect, the above reactions were extended to the whole polyimide model until the kinetic energy of the system was completely dissipated. The mechanical interlocking effect stemming from the ion chelation reaction greatly improves the interfacial adhesion strength. The enhancement of interface adhesion could alleviate the strain concentration caused by the local delamination due to external deformation, thus inhibiting the crack initiation of polymer-based coatings. In addition, the γ (Ni-Cr) alloy transition layer deposited by filtered cathode vacuum arc (FCVA) had excellent flexibility and ductility, which advantageously supported the subsequent growth of Cu film and enhanced the cooperative deformation ability. During the process of the FCVA deposition, the target was highly ionized, and the stress evolution could be optimized by ion irradiation and adsorbed atoms movement. Strong ion bombardment promoted local epitaxial growth and solid solution state transition at the interface, which was conducive to improving the interface adhesion strength and reducing the interface stress. The adhesion strength between NiCr alloy layer and polyimide assessed by 45° peel test was (1.75±0.16)N/mm, while no crack initiation or spalling was detected in the high deformation area of refined flexible copper clad wire after 1 000 folding tests. Therefore, the mechanical stability of FCCL can be significantly improved through the technical coupling of MEVVA ion implantation and FCVA, which is also expected to be applied to the industrial preparation of upmarket flexible copper clad laminate.