In this study, influences of surface hydrophobisation by surfactant vinyltrimethoxysilane (vtmos) on performance of carbon-based electrochemical capacitors were examined. Two distinct affecting mechanisms may be involved and coexist in the vtmos-modified carbon material, namely, the improvement mechanism and deterioration mechanism. The improvement mechanism suggests that the wettability of carbon material should be improved after surface hydrophobisation due to enhanced affinity to non-aqueous electrolyte solution. Improved wettability decreased mass transport resistance and increased accessible surface area for electric double layer formation and accordingly improved capacitor performance. The deterioration mechanism supposes that steric hindrance from grafting of large vtmos functional groups may have a negative effect on mass transport, especially in the case of high vtmos concentration. An effective vtmos concentration range was experimentally estimated as 0.15–0.35wt% for a great improvement in capacitor performance. The vtmos-modified activated carbon aerogel exhibits an excellent and comparable cycling stability to the original one.