Abstract: Graphene is widely used as an electrode material for supercapacitors, due to the high specific surface area, excellent electrical conductivity, and good chemical stability. However, during practical preparation and application, rough surface structures are often observed on graphene, including wrinkles and deformations. Their regulatory effects on the electrode/electrolyte interface properties need to be further clarified. In this work, flat graphene electrode models and wrinkled graphene electrode models with different amplitudes were constructed. The interfacial structures and capacitive responses in 2 mol/L NaCl aqueous solution were investigated by constant-potential molecular dynamics method. The results show that the wrinkled structures weaken the regular layered distribution of water molecules and Na⁺/Cl⁻ near the interface. Density peaks are decreased in height, broadened in width, and shifted outward. More pronounced multi-peak features are observed with increasing amplitude. Further analyses were performed using two-dimensional density distributions and water orientation analyses. It was revealed that the trough regions are more likely to induce local enrichment of counterions and dipole rearrangement of interfacial water. The orientation of water molecules and their hydrogen bonding are uneven in space. Accordingly, the way the electrolyte side balancing charge also clearly depends on the surface shape. The charge rearrangement induced by applied potentials is mainly confined to the electrical double-layer region. This rearrangement is determined jointly by ion enrichment and dipole responses of water molecules. Higher capacitance is exhibited by wrinkled electrodes than by flat electrodes. Stronger charge responses are shown in high-amplitude systems. The formation of heterogeneous electrical double layers and the charge compensation mechanisms induced by wrinkles are systematically elucidated in this paper. Theoretical foundations are provided by these findings for the morphology control of graphene-based supercapacitor electrodes and for the design of green energy storage devices.