This paper presents a simulation of 3D crystallization of colloidal nanoparticles on a substrate during drying. The translational motion and the rotational motion of nanoparticles are modeled by Langevin equation and the law of angular momentum conservation, respectively. Contact force, capillary force, Brownian force, van der Waals force, electrostatic force and fluid drag force are taken into consideration. The drying of colloid is expressed as a decrease of the colloid thickness with time. The drying process of a water solution of polystyrene nanoparticles on a flat substrate is investigated, so that a self-ordered 3D crystal of polystyrene nanoparticles is formed after drying. The crystallization is visualized with time, and vertical and planar structures of nanoparticles are evaluated temporally and quantitatively. The result indicates the primary mechanism of 3D crystallization of colloidal nanoparticles during drying, in which both layering in the vertical direction and planar crystallization take place at the same time.