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A novel interface architecture was constructed by a large aggregated pore of carbon nanotube (CNT) captured cyclodextrin (CD) with a small cavity. The isomer recognition ability of various cyclodextrin-incorporated carbon nanotube electrodes (CD-CNT/E) were firstly investigated and characterized systematically by differential pulse voltammetry experiments. Due to the functionalization of CNT with CD, modified electrodes exhibited perfect electrocatalytic response and enhanced recognition ability towards neutral nitrophenol (NP) isomers. The results indicated that α-CD-CNT/E had the best response to p-NP, γ-CD-CNT/E did best for o- N P and HP-β-CD-CNT/E showed excellent response to m- and p-NP, which originate from the porous structure of aggregated CNT, size selective effect and steric hindrance effect of substituent of CD. The electronic properties of CNT coupled with the specific recognition properties would indeed make for an ideal sensor.