Multi-wall carbon nanotube (MWNT)-modified glassy carbon electrodes (GCE) were prepared for simultaneous determination of rutin and quercetin. Microbial carbohydrates, $alpha$-cyclosophorohexadecaose ($alpha$-C16) and succinoglycan monomer M3 (M3) were doped into MWNTs to prepare a $alpha$-C16-doped MWNT-modified GCE (($alpha$-C16 + MWNTs)/GCE) and a M3-doped MWNT-modified GCE ((M3 + MWNTs)/GCE), respectively. The sensitivities of the ($alpha$-C16 + MWNTs)/GCE to rutin and quercetin were 34.7 ${mu}Acdot{mu}M^{-1}{cdot}cm^{-2}$ and 18.3 ${mu}Acdot{mu}M^{-1}{cdot}cm^{-2}$, respectively, in a linear range of $2sim8{mu}M$ at pH 7.2. The sensitivities of the (M3 + MWNTs)/GCE was 2.44 ${mu}Acdot{mu}M^{-1}{cdot}cm^{-2}$ for rutin and 7.19 ${mu}Acdot{mu}M^{-1}{cdot}cm^{-2}$ for quercetin without interference.