In heterogeneous catalysis, supported single-atom, single-cluster, and nanocatalysts have attracted wide attention. The interaction of single atoms and single clusters with support determines the stability and activity of the catalysts. To understand the type and strength of metal–support interaction, the adsorption structures and energies of transition metals (Mn = Fe, Ru, Os, Co, Ni, and Cu, n = 1–6) on the fully dehydrated silica (001) surface have been systematically computed based on spin-polarized density functional theory (GGA-rPBE-D3). It is found that aggregated structures are more stable than singly dispersed structures, indicating stronger metal–metal interaction. The adsorption energy increases from Fe, Ru to Os, while decreases from Fe, Co, Ni to Cu. Electron transfer from the metal to support has been found for Fe, Co, Ni, and Cu, while that from the metal to support and within the metal cluster has been found for Ru and Os, indicating the additional polarization and electrostatic interaction.