The conformational equilibria of naphthalene-viologen compounds linked with a flexible polymethylene bridge [-(CH2)n-: n = 3, 5, 7, 9, 12] were examined by NMR spectroscopy and molecular modeling. The chemical shift of the donor-acceptor dyad molecules depends on the linkage length and concentration. The equilibrium constants for the intramolecular and the intermolecular complexation were obtained from the chemical shift variation with concentration at high salt concentration. The complexation-induced chemical shifts (CISs) of the intra- and intermolecular complexes are obtained for molecules of n = 3 and 5. The molecules with longer linkages (n = 9 and 12) show aggregation behavior and the critical coagulation concentrations were obtained as 1.7 and 10 mM, respectively. Comparing the NMR results with molecular modeling calculations indicates that the naphthalene moiety can take various positions and orientations with respect to the bipyridinium moieties depending on the length of the linkage.