On the basis of formation of pseudorotaxane complexes between triptycene-derived tetralactam macrocycles 1 a and 1 b and squaraine dyes, construction of squaraine-based rotaxanes through clipping reactions were studied in detail. As a result, when two symmetrical squaraines 2 d and 2 e were utilized as templates, two pairs of isomeric rotaxanes 3 a–b and 4 a–b as diastereomers were obtained, owing to the two possible linking modes of triptycene derivatives. It was also found, interestingly, that when a nonsymmetrical dye 2 g was involved, there existed simultaneously three isomers of rotaxanes in one reaction due to the different directions of the guest threading. The 1H NMR and 2D NOESY NMR spectra were used to distinguish the isomers, and the yield of rotaxane 5 a with the benzyl group in the wider rim of the host 1 a was found to be higher than that of another isomer 5 b with an opposite direction of the guest, which indicated the partial selection of the threading direction. The X-ray structures of 3 b and 4 a showed that, except for the standard hydrogen bonds between the amide protons of the hosts and the carbonyl oxygen atoms of the guests, multiple π⋅⋅⋅π stacking and CH⋅⋅⋅π interactions between triptycene subunits and aromatic rings of the guests also participated in the complexation. Crystallographic studies also revealed that the rotaxane molecules 3 b and 4 a further self-assembled into tubular structures in the solid state with the squaraine dyes inside the channels. In the case of 4 a, all the nonsymmetrical macrocyclic molecules pointed in one direction, which suggests the formation of oriented tubular structures. Moreover, it was also found that the squaraines encapsulated in the triptycene-derived macrocycles were protected from chemical attack, and subsequently have potential applications in imaging probes and other biomedical areas.