Batch adsorption and desorption of crystal violet (CV) and basic red 9 (BR9) on multi-walled carbon nanotubes (MWCNTs) were conducted. To investigate the possible mechanisms of adsorption/desorption hysteresis, oxidized MWCNTs (O-MWCNTs) with more oxygen-containing groups were obtained by oxidizing as-purchased MWCNTs (A-MWCNTs) using nitric acid. The adsorption kinetics could be described by the pseudo-second-order model, suggesting that chemical reactions are the rate-limiting steps. The adsorption isotherms were fitted well by the Langmuir model, which suggests that, in addition to π–π interactions, chemical reactions significantly affect the adsorption. The adsorption capacity decreased in the order of CV on A-MWCNTs, BR9 on A-MWCNTs, and BR9 on O-MWCNTs, possibly because the amidation between BR9 and the surface groups of MWCNTs results in steric hindrance, which limits the adsorption of BR9 to inner grooves between CNT bundles. Adsorption/desorption hysteresis was observed for BR9 but not for CV. It was found that the π–π interaction and molecular entrapment were not responsible for the adsorption/desorption hysteresis. The hysteresis might be caused by the irreversible amide bonds between BR9 and MWCNTs. The results indicate that the steric hindrance due to the three-dimensional structure of organic compounds plays an important role in both adsorption/desorption kinetics and equilibria.