We have investigated the oxidation effect of multi-walled carbon nanotubes (MWNT) as electrode materials on the performance of an aqueous electrochemical double layer capacitor (EDLC). Carboxyl groups showing hydrophilic properties were mainly introduced on the MWNT surface by oxidation with an extremely aggressive oxidizing agent such as mixed acid H2SO4/HNO3. The hydrophilicity of MWNT increased with oxidation time, promising increased capacitance due to a good wettability to the aqueous electrolyte. In contrast, the surface structure disruption resulting from excessive treatment leads to the simultaneous decrease in the conductivity of the MWNT electrode, causing deterioration in EDLC performance. The balance between hydrophilicity and conductivity is therefore a key factor when designing improved electrode materials for EDLC. In this study, we found that specific capacitance was increased with oxidation times within 60min (dominant region of hydrophilicity increase), but decreased with times of more than 60min (dominant region of conductivity decrease). These results were identified with several analyses, such as Fourier transform-infrared (FT-IR) spectrometry, Boehm titration, N2 adsorption, water vapor adsorption, transmission electron microscopy (TEM), Fourier transform-Raman (FT-Raman), 4-probe IV measurement, and cyclic voltammetry (CV).