Silica nanoparticles have been receiving more attention from diverse research areas recently due to their significant physical properties such as large pore volume and high internal surface area, colloidal stability, high biocompatibility, and tunable pore sizes. These silica nanoparticles are great candidates for drug delivery applications because they can transport a large amount of drugs into selective organs and tissues due to their high surface area and large pore volume. However, there are important drug delivery mechanisms that need to be understood properly such as cellular uptake, endosomal escape, drug loading and release, and crossing physical barriers. Physicochemical properties of nanoparticles (size, shape, surface charge, or surface chemistry) are important for understanding these mechanisms in order to develop successful drug delivery applications. This research investigates how these surface charge properties change with different particle, pore diameters, roughness structure on the nanoparticle surface, and different temperature and solution conditions. Also, we investigate how the surface charging behavior of rough nanoparticles interacts with a flat plate. Rough nanoparticles and their interactions with surfaces theoretical assumptions can be wrong and ionic distribution can show variation locally. In order to calculate ionic distribution and surface charge properties in these systems, proper equations and boundary conditions were employed. The charge regulation model was used as a boundary condition because of the electric double layer overlap effect. Results showed that there was a considerable variation on surface charge properties due to the roughness structure with different roughness and particle sizes and temperature difference.