A low-energy Ar+ ion beam was used to modify the surface of a polyetheretherketone (PEEK) film. The modification reaction proceeded with or without oxygen gas injected during the irradiation. The surface functional groups of the modified PEEK were confirmed with X-ray photoelectron spectroscopy as increasing various oxygen-containing functional groups. The concentration of the functional groups varied rapidly with the irradiation time, reached a maximum value, and then slowly decreased. The surface morphology of PEEK was substantially changed by ion-beam irradiation. Surface smoothening occurred so that the surface roughness reached almost constant value after some irradiation time. The incorporation of functional groups on the PEEK surface and the surface topology change had opposite effects on the adhesion strength between PEEK and copper. Dominance of the former was evident because the lap-shear strength initially increased with the irradiation. The special surface features significantly enhanced the adhesion strength between the evaporated copper layer and the modified PEEK surface. However, the decrease in the surface roughness with a long time irradiation implies a decrease in adhesion strength due to a smaller contact area, and the shear strength due to topology change also slowly decreased after a long time irradiation.