A three-dimensional structure formation simulator of colloidal nanoparticles during drying is developed. Motion of the nanoparticles is modeled by Langevin equation, in which forces exerted on each nanoparticle consist of contact force, capillary force, Brownian force, van der Waals force, electrostatic force and fluid drag force. Drying of the colloid is expressed by a decrease of the thickness of a colloid film. The present simulator is applied to a drying process of the colloid film on a flat substrate, so that a multilayer structure of nanoparticles is formed. The structure formation is visualized with time, and the vertical and the planar structure of nanoparticles are evaluated temporally and quantitatively. The result indicates a mechanism of multilayer structure formation of colloidal nanoparticles during drying.