The nanometer-sized space formed in the porous material gives rise to a significant effect on the physicochemical properties of the condensed matter confined therein. It is well-known as the “confinement effect”, and it has been extensively interested in the relation between the size of the space and the structure and physical properties of the confined molecular assembly. We found that the adsorbed benzene molecules show two phase transitions in an isoreticular metal-organic framework-1 (IRMOF-1). Solid-state NMR and molecular dynamics simulation revealed that the molecular reorientation and intra-cavity migration of benzene take place in the two kinds of cavity in IRMOF-1 in the low and intermediate temperature phases. In the intermediate temperature phase, dynamic disorder of benzene occurs in the smaller cavities, accompanying partial melting of benzene in the smaller cavities. In contrast, in the high temperature phase the translational diffusion of benzene takes place over all the cavities. This fact suggests the phase transition is closely concerned with melting of the confined benzene. In this review, we describe the unique structure and physical properties of molecular assembly adsorbed into IRMOF-1 through the molecular motion and phase transition of benzene.