Carbon nanotubes (CNTs) from different sources were dissolved in water with high solubility by Congo red (CR) via strong noncovalent pi-stacking interactions. The resulting CNTs were capable of forming uniform, compact, stable films on various substrates. This provided a chance to explore the relationship between the surface property of CNTs and the adsorptive behavior of analytes on CNTs without considering the influence of film structures or free additives. Electrochemical behaviors of several small biomolecules and glucose oxidase (GOD) on various CR-functionalized. CNT films were examined. The results showed that both the hydrophobic structural defect sites and the hydrophilic oxygen-containing groups were the electroactive sites of CNTs, which was further proven by UV-vis and FTIR spectra. Moreover, the surface properties of CNTs could be conveniently designed by simple pretreatments for optimizing the adsorption and the electrochemical response of analytes. For instance, the hydrophobic defect sites created during the growth or the workup of CNTs were favorable to the adsorption and the electrochemical response of hydrophobic analytes, whereas the hydrophilic oxygen-containing groups produced by acid treatment facilitated the stable adsorption and the direct electrochemistry of redox proteins.