AbstractAsymmetric deformation density analysis is applied on bilayer graphene flakes as molecular capacitors to identify the extent of asymmetric distribution of electrons and holes when exposed to bias voltage. Three triangular, orthorhombic, and hexagonal symmetries for graphene flakes are considered in two sizes and electric field potential is applied along the vector perpendicular to graphene flakes' plane to simulate 1–4 V as the bias voltage applied to molecular‐scale capacitors The number of electrons responsible for asymmetric distribution of electrons and holes, and occupied to virtual transfer are calculated, and electric field deformation density analysis is also performed that shows distributions of electrons and holes are quite asymmetric for the orthorhombic symmetry, while for the other symmetries, they are almost image of each other. It was found that isosurfaces of deformation density distribution possess a multilayer structure and accretion and depletion of electrons can be taken place between flakes or outside the parallel flakes, and it is shown that bias voltage is able to significantly remove symmetry of electrons and holes distribution. Inspection of molecular orbitals showed that electric field could change the energetic order of molecular orbitals, so that occupancy inversion is occurred for the orthorhombic systems that is responsible for their extraordinary properties.