A novel cooperative pseudo[3]rotaxane system was successfully constructed by the inclusion complexation of two identical amine naphthotubes with a bis-pyridinium/isoquinolinium guest. Single crystal structure analysis revealed that weak Csp3-H⋯O hydrogen bonds between the two hosts are responsible for the positive cooperativity during the formation of pseudo[3]rotaxanes. Moreover, intermolecular charge-transfer interactions between the electron-rich host and the electron-poor guests were observed. The pseudo[3]rotaxanes showed pH-controllable association/dissociation processes with naked-eye color changes in solution.