An EMD model for nanocolloidal dispersions considering the interaction between atoms within solid particles is developed for viscosity calculation and studying the effect of the particle size and volume fraction. Strong oscillations are observed in the pressure tensor autocorrelation function. Elimination of this oscillation is achieved by adjusting the potential among atoms of nanoparticles to reduce the acoustic mismatch between particles and liquid. The shear viscosity of nanocolloidal dispersion is found strongly dependent on the particle size, which cannot be predicted by traditional effective medium theory. Through decomposing of the pressure tensor, the viscosity contribution from interactions between liquid-solid atoms and solid-solid atoms are believed to dominate the viscosity increase of colloidal systems. Our model reveals the shear viscosity increase mechanism at the molecular-level and predicts that the shear viscosity of simple colloidal dispersions reaches a plateau value when the particle size becomes large enough.