Developing highly holey graphene with controllable doping enhances ionic transport and conductivity, boosting the performance of energy storage devices like supercapacitors. However, the method for precise site-selective doping and the effects of heterogeneous atomic doping at pore edges on ion transport remain not fully understood. This study presents a method to achieve precisely and selectively high nitrogen doping (N-doping) at the hole edges of porous graphene (N-EHG) through a two-step process. Compared to untreated graphene (HG) and basal plane-doped graphene (N-BHG), N-EHG demonstrates superior charge storage capacity and ionic conductivity. Analyzing the porous structure, size distribution, and hydrophilicity influenced by the carbon–oxygen ratio, N-EHG shows a specific surface area of 509 m² g⁻¹, significantly higher than HG's 100 m² g⁻¹. Electrochemical results revealed that N-BHG and N-EHG achieved high gravimetric capacitances of 482.3 and 624.4 F g⁻¹, respectively, due to enhanced ion diffusion, exceeding HG by ≈12- and 15.6-fold. Furthermore, the assembled coin-cell retains over 99% capacitance after 15,000 cycles, demonstrating exceptional stability. Both N-EHG and N-BHG show diffusion-governed charge storage, with N-EHG benefitting further from edge-state N-doping. Density Functional Theory (DFT) calculations reveal a lower energy barrier for ion diffusion and strong K⁺ adsorption on edge pyridinic-N, where increased electrode charge creates a negative center on N-dopants, enhancing K⁺ binding. These findings underscore the potential of edge-state N-doping in holey graphene for advanced energy storage applications.