The design of nanoporous anodic aluminum oxide (AAO) substrates and processes for template-assisted self-assembly (TASA) of nanoparticles using the spin-coating method is important to form controllable non-close-packed (NCP) monolayer arrays of nanoparticles over large areas. In this study, the effects of varying particle sizes and concentrations in silica nanoparticle (SN) dispersions and the pore sizes of nanopores on the AAO substrates on the particle loading density of SN monolayer arrays were investigated. When the pore sizes were close to the particle sizes, in the range of 108–435 nm in diameter, we demonstrated that the particle loading density was dependent on the particle number concentration in a film of the SN dispersions with a thickness of ca. 2 μm. As a result of coating different size SNs on AAO substrates with varying pore size, it was found that the particle loading densities varied and had the maximum value around a particle size/pore size ratio of 1.5. In addition, lower loading angles of the SNs on the nanopores caused by a mismatch between the particle size and pore size tended to cause the SNs to move on the substrates when the particle size/pore size ratio was higher than ca. 1.5.