The structural properties and thermal stability of Si-doped amorphous indium oxide (ISO) were investigated via experimental characterization and computational modeling techniques. The total structure factors, S(Q), and reduced pair distribution functions, G(r), were calculated for both annealed and pristine ISO samples, revealing the distinct structural features induced by Si doping and thermal treatment. Although the pristine ISO samples exhibited halo patterns indicative of an amorphous structure, annealing at 600°C led to pronounced Bragg peaks, suggesting that the sample was crystallized. However, an ISO with a higher Si content (20 at.%) retained its amorphous structure even after annealing, highlighting the role of Si-doping in enhancing the thermal stability. Classical molecular dynamics–reverse Monte Carlo simulations were employed to elucidate the structure of pristine ISO samples, revealing good agreement with the experimental data. Furthermore, the partial structure factors, Sij(Q), and partial pair distribution functions, gij(r) demonstrate the influence of Si doping on atomic correlations and density changes in the ISO. Polyhedral connectivity analysis suggests that the fraction changes of edge sharing due to Si doping affect the thermal stability of ISO and that SiO4 tetrahedra play a crucial role in inhibiting crystallization.