A single sheet of Si nanoclusters with an average diameter of about 2 nm has been formed in a 30 nm Si/7 nm SiO2/Si layer stack by 50 and 60 keV Si+ ion-beam mixing at room temperature and fluences between 8.5 ⋅ 1015 and 2.6 ⋅ 1016 ions/cm2 and by subsequent thermal annealing at a temperature above 1000 °C. Computer modeling of the process is accomplished by TRIDYN dynamic ballistic simulation of ion mixing and subsequent lattice kinetic Monte Carlo simulation of the phase decomposition of substoichiometric silicon oxide into Si nanoclusters in a SiO2 matrix. The simulation algorithms are briefly described with special emphasis on the choice of governing parameters for the present system. In comparison to the experimental results, it is concluded that the predicted ion mixing profiles overestimate the interface broadening. This discrepancy is attributed to the neglect of chemical driving forces in connection with thermal-spike induced diffusion, which tends to reconstitute the Si/SiO2 interfaces. With a corresponding correction and a suitable number of Monte Carlo steps, the experimentally obtained areal densities and average diameters of the nanoclusters are successfully reproduced.