Natural cyclodextrin (CD) macrocycles are known to form diverse inclusion complexes with a wide variety of organic molecules, but recent work has revealed that inorganic clusters also form multicomponent supramolecular complexes and edifices. Such molecular assemblies exhibit a high degree of organization in solution governed by various chemical processes including molecular recognition, host-guest attraction, hydrophobic repulsion, or chaotropic effect. Nuclear magnetic resonance (NMR) spectroscopy is one of the most efficient and practical analytical techniques to characterize the nature, the strength and the mechanism of these interactions in solution. This review provides a brief overview on recent examples of the contribution of NMR to the characterization of hybrid systems in solution based on CD with polynuclear clusters, including polyoxometalates (POMs), metallic clusters and hydroborate clusters. The focus will be first on using 1H (and 13C) NMR of the host, i.e., CD, to identify the nature of the interactions and measure their strength. Then, 2D NMR methods will be illustrated by DOSY as a means of highlighting the clustering phenomena, and by NOESY/ROESY to evidence the spatial proximity and contact within the supramolecular assemblies. Finally, other NMR nuclei will be selected to probe the inorganic part as a guest molecule. Attention will be paid to classical host-guest complexes Cluster@CD, but also to hierarchical multi-scale, multi-component assemblies such as Cluster@CD@Cluster.