Supramolecular complexes between cyclodextrin and iron species are studied by using secondary ion mass spectrometry. The iron species are prepared by pulsed-laser ablation of bulk iron in water, providing Fe+ (56 m/z) and FexOy+ (x, y=1–7) species. Cyclodextrin is added to the water either before or after the laser ablation. A matrix enhanced secondary ion mass spectrometry for improving the sensitivity of high mass molecular analysis can be applied for cyclodextrin (C42H70O35, 1134 u). The fullerene 30 films deposition matrix enhanc the intensity of cationized cyclodextrin with Na by a factor of 37 and the deprotonated cyclodextrin increases by factor of 100 and its C8H7O fragment by factor of 10. When cyclodextrin is added after laser ablation, the relevant peak at 1210 m/z is observed and assigned as C42H67O35FeNa+. Two possible explanations represent the host–guest C42H67O35Na–Fe complex, in which Fe is in the cavity, or the adduct C42H67O34Na–FeO with FeO on the outer surface. Such supramolecular complexes have application potential as surface nanostructures in functional devices. The complex combination of thiolated cyclodextrin, chemisorbed on gold surface, with deposited iron species is studied (Au-S-CD/Fe). The AuxHySz clusters, fragments with origin in cyclodextrin molecule associated with Au, and molecular ions are observd. The group of AuxHySz(x = 2–17, y = 0–2, z = 1–5) clusters have higher intensities than other species. Using laser ablation in water, the solution of iron species is dropped on Au-S-CD, where mass peaks at 1227 m/z, 1243 m/z, and 1260 m/z are observed and assigned to C42H68O34SNa-Fe+, C42H68O34SK-Fe+ together with C42H68O34SNa-FeO+, and C42H68O34SK-FeO+, respectively.