Polyimide films are widely used in various industrial fields. Some typical products are flexible printed circuits (FPCs), flexible displays, and electronic papers. Good adhesion between metal thin films and polyimide films is required for their long lifetime. Ion beam irradiation to the polyimide films modifies the chemical compositions, the chemical states, and the surface nanomorphology. These modifications are potential techniques to improve the adhesion. In this study, the authors employed a linear ion source, which is able to irradiate ion beam on large surfaces homogeneously. The linear ion source is desirable for industrial usage because of its high productivity. The aim of this work was to investigate the effect of modification using the linear ion source. The chemical states of the interface were characterized using x-ray photoelectron spectroscopy (XPS). The surface nanomorphology was investigated by atomic force microscopy (AFM). The performance of the modification system will be discussed, and the characteristics of the modified polyimide will be investigated in detail.