The geometric and electronic properties of Bi-adsorbed monolayer graphene, enriched by the strong effect of a substrate, are investigated by first-principles calculations. The six-layered substrate, corrugated buffer layer, and slightly deformed monolayer graphene are all simulated. Adatom arrangements are thoroughly studied by analyzing the ground-state energies, bismuth adsorption energies, and Bi-Bi interaction energies of different adatom heights, inter-adatom distance, adsorption sites, and hexagonal positions. A hexagonal array of Bi atoms is dominated by the interactions between the buffer layer and the monolayer graphene. An increase in temperature can overcome a ∼50 meV energy barrier and induce triangular and rectangular nanoclusters. The most stable and metastable structures agree with the scanning tunneling microscopy measurements. The density of states exhibits a finite value at the Fermi level, a dip at ∼-0.2 eV, and a peak at ∼-0.6 eV, as observed in the experimental measurements of the tunneling conductance.