Abstract: Graphene is acknowledged as one of the ideal active electrode materials for electric double-layer capacitors because of its extremely high specific surface area and outstanding electronic conductivity. By introducing defects or heteroatoms into the graphene sheet, the electronic structure around the defects can be altered, which could lead to an increased quantum capacitance (C_Q) and therefore te capacitive performance. One of the unavoidable problems for manufacturing and using graphene materials is that the stacking of the layers affects their electronic structure, and eventually their capacitance. DFT calculations were used to investigate the effect of layer stacking in bilayer graphene materials on C_Q and the surface charge density. A two layer, AB-stacked graphene model, in which the top layer is defective and the bottom one is perfect was assumed for the calculations. The defective graphenes investigated are those containing Stone-Thrower-Wales defects, single vacancies (SV), three with double vacancies (5-8-5, 555-777 and 5555-6-7777), pyrrole-N graphene and the pyridine-N graphene. Results indicate that both the values and waveform of C_Q of the materials are changed by stacking. The C_Q values of most of these graphenes are significantly increased after stacking. The C_Q waveforms of the SV and N-doped graphene are relatively insensitive to stacking. The basal layer contributes a considerable amount of charge, which is most obvious for the pyrrolic-N double-layer graphene and 5-8-5 double-vacancy graphene. The surface charge density provided by the defective top layer is increased by interlayer interaction, especially for the N-doped graphene. The uniform distribution of charge on the bottom layer partially alleviates fluctuations in the C_Q waveform. These findings provide theoretical guidance for the micro-structural design of graphene materials to optimize their performance as electrode active materials.