Nanostructures are used for various chemical, biological, and even volatile organic compound (VOC) sensor applications, in which the inkjet printer provides an easy and convenient fabrication method. In particular, nanoparticles in injected droplets form various self-assembled nanostructures after evaporation such as flat films, rings, and domes, whose patterns are largely influenced by the flow fields within those droplets, temperature, humidity, and substrate wettability. In addition, the temperature at the liquid–gas interface of the droplets governs the local surface tension and evaporation flux, thereby determining the convection fluid flow and particle movement. In this study, we investigate four particle deposition patterns via numerical simulations. First, we reveal the formation of monolayered flat-films on a superhydrophilic substrate in the constant contact angle (CCA) mode during evaporation. Second, we confirm that particles in evaporated droplets usually form coffee-ring patterns on a hydrophilic substrate, which are mainly governed by capillary flows. Interestingly, we find that the coffee rings with low aspect ratios appear to be well-ordered in the constant contact radius mode, while those with high aspect ratios appear to be non-uniformly self-assembled in the CCA mode in an amorphous structure. Third, we prove that the Marangoni flow generated on a hydrophobic substrate accumulates particles at the center of the droplet, forming well-ordered dome-shaped patterns. Furthermore, we experimentally demonstrate four different particle deposition patterns to validate our simulation results and confirm that both sets of results are in reasonable agreement with each other. Hence, we believe that these theoretical model and simulation results can help to develop various nanostructure-based sensor applications by enhancing their performance.