The change in the structure of zinc nanoparticles (NPs) in the Si matrix after irradiation with swift Xe ions is analyzed. Silicon wafers were implanted with 64Zn+ ions at a dose of 5×1016/cm2 and energy of 50 keV at a temperature of 350°C. After implantation in Si, zinc NPs with a size of about 10 nm were formed. Then the samples were irradiated with swift Xe ions with an energy of 167 MeV and fluences of 2×1013 and 5×1014/cm-2. The samples were studied by X-ray absorption spectroscopy (XAS) on the K-edge of Zn. According to XANES data, in samples with different Xe fluences, zinc has a similar local environment and exists in the metallic phase. According to EXAFS data, the intense peak of the Fourier transform is in the range of 2–3 Å and corresponds to the split first coordination sphere in the Zn structure. After irradiation with Xe, the intensity of this peak noticeably decreases compared to the sample after Zn implantation, which indicates a very strong disordering of the local structure, which is characteristic of small NPs with sizes less than 5 nm.