The incorporation of active sites into metal-organic frameworks (MOFs) or porous coordination polymers (PCPs) is an attractive way to functionalise these materials. However, the methodology to organise substitution-inert metal-based secondary building units (SBUs) with active sites into MOFs or PCPs via coordination driven self-assembly is severely limited. In this study, we successfully assembled substitution-inert paddle-wheel Rh(II) dimers to afford three novel porous frameworks, Rh2(ppeb)4(THF)2 (1-THF), Rh2(ppeb)4(3-pentanone)2 (1-PN) and Rh2(ppeb)4(1-adamantylamine)2 (1-AD) (ppeb = 4-[(perfluorophenyl)ethynyl]benzoate), by using non-covalent interactions. Multipoint arene-perfluoroarene (Ar-Ar(F)) interactions, which allow the unidirectional face-to-face interaction mode of aromatic rings, were used to assemble the substitution-inert paddle-wheel Rh(II) dimers. The obtained frameworks were structurally characterisation by single crystal X-ray diffraction, and it is found that all structures exhibited a one-dimensional channel with active axial sites exposed to the pores. The porous properties of the obtained frameworks were also investigated by thermogravimetric analysis, gas adsorption and powder X-ray diffraction measurements. Moreover, the ligand substitution reaction at the active axial sites was examined at the crystalline state and the flexible structural transformation with the change of channel shapes and sizes was observed.