In this paper we describe copper clusters and nanoparticles formation by the reduction of copper (II) ions inside cavities of macrocycle molecules using supramolecular compound [Cu(Cyclen)(H2O)@CB[8]](NO3)2·12H2O followed by Cu atoms diffusion between macrocycle CB[8] molecules. To understand the copper cluster genesis and nanoparticles formation x-ray powder diffraction (XRD), electron paramagnetic resonance (EPR), FTIR-spectroscopies, HRTEM and thermal analysis were used. It was found that atomic Cu(0) was not fixed in the cavity under heating, and Cu clusters and nanoparticles were formed by heating of supramolecular compound powder at 200–340°C in He, but more preferably in H2. The process was partially reversible after heating the powder up to 300°C for 15min and air exposure for a few months. The process was irreversible after heating of the sample at temperatures higher than 340°C due to CB[8] cavitand decomposition. In general, exposure of the samples to air leads to oxidation and hydration clusters of Cu. Nanoparticles up to 600nm in size formed on the surface of agglomerated polycrystalline powder at temperatures lower than 200°C. The clusters less than 7nm and 40nm in size were formed at 300°C inside and outside agglomerating polycrystalline powder, respectively. The diffusion coefficient of copper atoms inside polycrystalline CB[8] agglomerates equal to 10−10cm2/s by heating the samples at 300°C was found.