The dispersion and aggregation behavior of surface-modified nanoparticles in organic solvents is investigated by numerical simulations based on the discrete element method. In the simulation model, the van der Waals attractive force, the force based on the mixing energy between the surface modifier and solvent, and the elastic repulsion force by surface modifiers are considered as the interactions between two nanoparticles, in addition to the contact force, hydrodynamic drag force, and Brownian random force. The effects of the surface modifier, the solvent, and the volume fraction of nanoparticles on the dispersion and aggregation behavior are investigated. Decanoic acid-modified nanoparticles are well dispersed in cyclohexane because of the high affinity of decanoic acid with cyclohexane, but aggregate in toluene because of their low affinity with toluene. Oleic acid-modified nanoparticles are dispersed in toluene because of their high affinity with toluene. Furthermore, a phase diagram indicating the dispersion and aggregation behavior of surface modified nanoparticles in toluene is projected onto the plane of the volume fraction of nanoparticles versus the interaction parameter between the surface modifier and solvent.