In a model system of an O-2-O-2 dimer confined in the nanopores of Cu-1,4-cyclohexanedicarboxylic acid, the molecular orientation associated with the spin state was observed by precise synchrotron radiation structure analysis. The obtained charge density level structures revealed that the molecular orientation varied with increasing temperature, coupling with the spin states of the O-2-O-2 dimer. The magnetic properties previously reported were consistently explained by the S = 1 dimer model taking into account the molecular arrangements. The obtained gap parameters are different from those of the O-2-O-2 dimer confined in the nanopores of Cu-2,3-pyrazinedicarboxylate-pyrazine, which is explained by the pore deformation due to the adsorption, depending on the pore size and/or flexibility of the coordination polymer.