Matusi–Akaogi force field is used in molecular dynamics simulations to generate three samples of amorphous TiO2 of 3-nm size under different heating and quenching rates. The averaged pair correlation functions, coordination numbers, bond lengths, bond angles, and dihedral angles are calculated at 315 K. It is found that overcoordinated Ti and O atoms are in the core region, 6- and 3-fold coordinated Ti and O atoms are in the central part, and undercoordinated Ti and O atoms are in the vicinity of the surface. The correlations are significant up to 10 Å and vanish at the particle size. The calculated averaged bond lengths for short-range interparticle correlations agree with the experimental data. The discrete bond angles and dihedral angles of crystalline sphere get distributed over complete range in the amorphous phase and closer strained atomic network is predicted. The relative variance in the atomic arrangements in three samples is within 4%.