MIL-53 (Al) is an important example of metal-organic frameworks (MOFs) with a flexible framework capable to efficiently separate ortho and para isomers of xylene at moderate temperatures. The MIL-53 MOF contains mobile terephthalate phenylene fragments that can be used as a dynamic probe to investigate the guest-host interactions and the origin of the separation selectivity. Here 2H NMR spin alignment echo technique for the first time was applied to probe ultraslow structural mobility (0.1-1 kHz) in MOFs materials, with particular application to MIL-53(Al) saturated with ortho or para isomers of xylene. A specific influence of different isomers of xylene adsorbed in the MOF pores on the rotation of the phenylenes in MIL-53 for the temperature range with proved separation selectivity (T < 393 K) is shown. It has been established that the rotation of phenylene fragments is sensitive to the type of xylene isomer. The phenylenes' rotation performs 1 order of magnitude slower in the presence of o-xylene (kortho = 70 s-1) compared to the same rotation in the presence of the other isomer, p-xylene (kpara = 800 s-1) at T ∼ 373 K. This is rationalized by a stronger interaction of the ortho isomer with the linker than the para isomer. This finding offers an understanding of the molecular mechanism of p- and o-xylene separation by MIL-53: stronger interaction of o-xylene with organic linker compared to p-xylene provides separation of these isomers on MIL-53.