A unique tubular molecular-assembly, constructed by β-cyclodextrin and Na[Ni(mnt)(2)], was identified by X-ray crystallography. Inclusion complex Na[Ni(mnt)(2)]@β-cyclodextrin (1) crystallized in space group P2(1)2(1)2 as hydrated head-to-head, tail-to-tail, and head-to-tail host pipelines with negatively charged [Ni(mnt)(2)](-) guests included, exhibiting a 3 : 1 (host : guest) stoichiometry. The hydrophilic transition-metal coordination compound (Na[Ni(mnt)(2)]) was embedded within a hydrophobic cyclodextrin cavity, which resulted in a β-cyclodextrin trimer motif and one-third "empty" host packing model in the crystal. Induced circular dichroism (ICD) spectra of inclusion complex 1 was investigated, which indicated the same penetration pattern of the guests in host cavities in solution phase as that discovered in the crystal structure. In addition, PM3 quantum chemistry calculations strongly supported the co-conformational alignments of inclusion complex 1 that was identified in the crystal as well as in the solution.