The structure formation of surface-modified nanoparticles during solvent evaporation is investigated by numerical simulation based on the discrete element method (DEM).The interaction forces induced by surface modifiers are considered, in addition to the contact force, Brownian force, capillary force, van der Waals force and hydrodynamic drag force. The effects of the solvent, the surface modifier and the surface coverage of the modifier on the structure formation process during solvent evaporation and the final structure of the nanoparticles on the substrate are clarified. When the affinity between the solvent and the surface modifier is high, the surface-modified nanoparticles are well-dispersed in the solvent and the structures of nanoparticles tend to be well-ordered after solvent evaporation. On the other hand, when the surface coverage of the modifier is fairly high, the final structures of surface-modified nanoparticles are relatively disordered even though the nanoparticles are dispersed in the solvent. Such a structure formation mechanism is explained based on the force curve between two nanoparticles during solvent evaporation.