The evolution of surface chemical structures of polyimide induced by Ar fast atom beam (Ar-FAB) bombardment and vacuum ultraviolet (VUV) irradiation was investigated using X-ray photoelectron spectroscopy (XPS) to clarify the activated sites for low-temperature hybrid bonding. These sites in molecular chains are considered corresponding to the bonding sites. They affect interfacial properties. Therefore, such analyses are necessary to optimize the processing parameters in different surface-modification methods. The XPS results demonstrated that Ar-FAB physical bombardment transformed the polyimide surface into benzene-dominant structures, whereas the effect of VUV irradiation was located at side chain groups such as ether and carbonyl, resulting in much longer molecular fragments (i.e., less matrix damage). Moreover, the calculated thickness of the VUV-induced modification layer grew to around 0.6 nm at its maximum.