The spatial distribution of binding states in the depth direction of a soft polydimethylsiloxane (PDMS) material was investigated in the hard skin layer formed by Ar ion-beam irradiation. The hard skin layer, typically considered silica-like and homogeneous, was heterogeneous, comprising a topmost layer and an intermediate layer. Impinging Ar ions transferred energy to the PDMS medium by collisional energy transfer, which was maximised at the surface and decreased gradually as the ions penetrated the PDMS. The decreasing energy transfer rate from the surface created a heterogeneous hard skin layer. X-ray photoelectron spectroscopic depth profiling showed the existence of the topmost and intermediate layers. In the topmost layer, scission and cross-linking occurred simultaneously; Si-O bonds showed the dissociated state of SiOx (x = 1.25-1.5). Under the topmost layer, the intermediate layer showed mostly cross-linking, with Si-O bonds showing silica-like binding states of SiOx (x = 1.75-2). The spatial distribution of carbon-related bonds such as C-Si and sp3 C-C also showed heterogeneity, yielding a gradient of bond distribution. A theoretical analysis of the collisional energy transfer rate and displacement per atom showed consistency with the XPS depth profiling results.