We investigated the wrinkle formation on ion-beam (IB)-irradiated substrates coated with the thermoplastic elastomer styrene-b-isoprene-b-styrene (SIS) and demonstrate a relation of the wrinkle structure and the newly formed top layer induced by IB. IB irradiation led to polymer cross-linking on the surface, thereby forming a new skin layer, a finding which was supported by an X-ray photoelectron spectroscopy analysis, Young moduli calculated using force-distance curves, and time-of-flight secondary ion mass spectrometry depth profiling. The wrinkle wavelength increased according to the irradiation time, which indicates that the latter mainly increased the thickness of the cross-linking layer. The increase in the wrinkle wavelength varied from 420 to 670 nm by changing the IB irradiation time. In this paper, we present not only the expectation of wrinkle fabrication using our method but also the possibility of choosing diverse materials such as the thermoplastic elastomer SIS for fabrication of wrinkle structures.