In this study, we compared two methods(an acid treatment in strong acid reflux and a heat treatment in air atmosphere) for hydrophilic surface treatment of multi-walled carbon nanotubes(MWNT) to enhance the capcity of $RuO_2$/MWNT composite electrode materials for ultracapacitor. Both treatments generated a number of defects on the surface of MWNT by the breakage of $pi$ bond in graphene layer at which carboxyl groups were introduced. However, the degree of hydrophilicity generated by strong acid treatment was higher than that by heat treatment in air, which was revealed by the quantitative measurement of surface carboxyl groups by using Boehm titration. The increased hydrophilicity save rise to an improved dispersity of $RuO_2$ nanoparticles on MWNT. Finally, the improved dispersity resulted in the capacity enhancement of composite electrode materials for ultracapacitor.