Self-assembled organic nanotubes (ONTs) have been actively examined for various applications such as chemical separations and catalysis owing to their well-defined tubular nanostructures with distinct chemical environments at the wall and internal/external surfaces. Adsorption of heavy metal ions onto ONTs plays an essential role in many of these applications but has rarely been assessed quantitatively. Herein, we investigated interactions between Cu2+ and single-/quadruple-wall bolaamphiphile-based ONTs having inner carboxyl groups with different inner diameters, COOH-ONT10nm and COOH-ONT20nm. We first examined the effects of Cu2+ on their nanotubular structures using SAXS, STEM, and AFM. COOH-ONT10nm was stable in aqueous Cu2+ solution in contrast to COOH-ONT20nm owing to the presence of polyglycine-II-type hydrogen bonding networks within its wall. Subsequently, we studied the Cu2+ adsorption behavior of COOH-ONT10nm by monitoring the concentration of unbound Cu2+ using linear sweep anodic stripping voltammetry. The Cu2+ adsorption was quick, attributable to efficient Cu2+ partitioning through the open ends of the ONT, followed by fast Cu2+ diffusion in the uniform, relatively large nanochannel. More importantly, the Cu2+ adsorption capacity and affinity of COOH-ONT10nm were measured under different pH conditions using the Langmuir adsorption model. The adsorption capacity was similar at the pH range examined, showing the participation of approximately 25% of the inner carboxyl groups in the adsorption. The adsorption affinity increased with pH, indicating the essential role of the deprotonated carboxyl groups in Cu2+ adsorption. Most interestingly, the Langmuir adsorption constant was significantly higher than those of previously reported synthetic adsorbents and planar monolayer based on carboxyl binding sites. The high Cu2+ affinity of the ONT was attributable to the highly dense binding sites on the well-defined nanoscale concave structure of the inner channel. These results provide a valuable guideline for designing self-assembled nanomaterials for efficient chemical separations, detection, and catalysis.