Herein, a comparative computational study inquiring about ground state magnetic properties of a nanometer‐size bowtie graphene quantum dot with an AA‐stacking bilayer trapezoid counterpart based on the single‐orbital Hubbard model and density functional theory (DFT) is presented. The structures have an antiferromagnetic ground state with a 1‐to‐1 correspondence between the local spin polarizations of the two systems. The tight‐binding energy spectra look different. However, a similar fashion in the energy spectra emerges after considering the Hubbard interaction term. A comparison between the spatial distributions of edge states shows that the wave functions in both structures are sublattice polarized by proposing a specific unit cell in the bilayer case. In addition, the on‐site coulombic repulsion consequence on the rising of magnetization and the size of the local magnetic moment has been considered.