Ionic liquids have been considered as promising electrolytes for supercapacitors due to the wide electrochemical stability window. However, water molecules inevitably damage the electrochemical properties of ionic liquids due to the hygroscopic property. This paper reveals the effect of water molecules on the interfacial structure and energy storage performance of ionic liquids using the atomistic simulations. Unlike neat ionic liquids, the Helmholtz region for humid ionic liquids is mainly composed of BMI cations and water molecules. Importantly, water molecules primarily accumulate in the buffer region between BMI cation and graphene electrode, especially at the high negative charges, which is the crucial factor to induce the hydrogen evolution reactions for the decreased electrochemical stability window. More interestingly, the dielectric properties of water molecules in the buffer layer are beneficial for lowering the electric potentials for higher capacitive performance. The differential capacitance of [BMI+][BF4−]/H2O electrolyte exhibits a bell-shaped curve with a maximum value of ~5.0 F/cm2 at 0.75 V. The revealed insights are important for understanding the water effect in ionic liquid-based supercapacitor energy storage.