The ability to control the size and the spatial properties of nanoparticle catalysts on the surface of a substrate or support material is critical in exploiting the unique activity of catalysts at the nanoscale. We report herein new findings of an atomic force microscopic investigation of the thermal activation of molecularly wired core-shell nanoparticle assemblies on flat surfaces toward the development of the ability of size and spatial control. Gold nanocrystals of similar to2-nm core size capped by alkanethiolate shells were assembled by covalent or hydrogen-bonding linkages onto mica and graphite substrates as a model system. The results show that the particle size and interparticle spatial properties are highly dependent on the chemical and physical nature of the linker molecule and the substrate. Such dependence is inherently linked to the surface mobility, surface tension, and adsorption energy of nanoparticles on the substrate, which are supported by the assessment based on the theoretical modeling of the thermally induced sintering process. The surface mobility and consequent size evolution can be effectively influenced by manipulating the surface property or morphology of the substrate and that of the nanoparticles (e.g., functional groups, hydrophobicity, surface steps, etc.). The implications of our findings on the controlled processing of nanostructures on catalyst-support materials and the fine tuning of the catalytic or electrocatalytic activities are also discussed.