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Molecular dynamics simulations were used to explain the origin and properties of electrical double-layer capacitance in short graphene nanochannels with width below 2 nm. The results explain the previously reported experimental result on the non-monotonic dependence of the capacitance with the channel width. The mechanism for the anomalous increase of the capacitance in sub-1-nm in pore diameter is attributed here to the width-dependent radial location of counterions in the nanochannels, and the restricted number of co-ions. Decrease of the channel width lowers the number of co-ions and positions the counterions closer to the channel walls. For nanochannels with width ranging from 1 to 2 nm, co-ions are allowed to enter the nanochannel, and both types of ions assume alternating layered distributions leading to the decrease of the capacitance. Voltage is another control parameter which allows understanding capacitance in graphene nanochannels. As the voltage increases, due to limited space near the charged surface, more counterions need to be located in the center of the nanochannel resulting in further capacitance decrease.