In microelectronics packaging, the reliability of the metal/polymer interface is an important issue because the adhesion strength between dissimilar materials is often inherently poor. This paper reports the peel strength and surface morphology of a Cu/Ni/PI structure flexible copper clad laminate (FCCL) based on polyimide(PI) according to the pre-treatment atmosphere and times. Field emission scanning electron microscopy (FESEM), x-ray diffraction (XRD), and x-ray photoelectron spectroscopy (XPS) were used to analyze the surface morphology, crystal structure and interface binding structure, respectively, of the sputtered Ni, Cu, and electrodeposited copper foil layers. The surface roughness of the Ni and Cu sputtered deposition layers and the crystal structure of the electrodeposited Cu layer changed according to the pre-treatment atmosphere and times of PI. The PI surface etching speeds and surface shapes differed according to the gas used in plasma preprocessing. The highest peel strength (mean 15.8 gf/mm) can be obtained in a preprocessing process for 400 seconds in an O2 atmosphere due to the increase in mechanical binding force and change in chemical binding structure caused by the increase in polyimide surface roughness.