The self-assembly of transition metal salts with 5-(pyridin-4-yl)isophthalate ligand and N-donor ligands affords a series of entangled coordination frameworks based on different metal cluster cores, namely, [Co(L)(H2O)2]·H2O (1), [Ni(L)(H2O)]·H2O (2), [Co4(L)2(SO4)(H2O)5(OH)2]·15.5H2O (3), [Co2(L)2(2,2′-bpy)2]2·H2O (4), [Co2(L)2(phen)2] (5), [Ni(L)(en)(H2O)2]2·2H2O (6), [Ni(L)(dap)]·3H2O (7), [Co(L)(bph)(H2O)2]·H2O (8), [Co(L)(bbm)0.5]·4H2O (9), [Co(L)(bimb)0.5]4·13H2O (10) [L = 5-(pyridin-4-yl)isophthalic acid; 2,2′-bpy = 2,2′-bipyridine; phen = 1,10-phenanthroline; en = ethane-1,2-diamine; dap = propane-1,2-diamine; bph = (1E,2E)-1,2-bis(pyridin-4-ylmethylene)hydrazine; bbm = 1,4-di(1H-imidazol-1-yl)benzene; bimb = 4,4′-di(1H-imidazol-1-yl)-1,1′-biphenyl]. Their structures were characterized by elemental analysis, IR spectra and TG analyses and further determined by single-crystal X-ray diffraction analysis. The auxiliary ligands play important roles in the formation of various entangled networks. 1–2 show a 2D layer network and its layers are held together by π–π stacking interactions and other unconventional interactions. Complex 3 displays an unusual Co4 cluster core which is linked by η1,η1,η1,μ3-SO42− and μ3-OH ions. Upon adding chelating ligands, 4–5 show 2D → 2D entangled polymers with polycatenated and polyrotaxane features based on 4,4-sql layers. 6–7 still exhibit layer strutures, although they have chelating ligands, which may be due to the absence of π–π stacking interactions. 8–10 present pillar-layer structures which are supported by different lengths of pillars. Three-fold interpenetration with polycatenated features are observed in 8–9. 10 exhibits a 4-fold interpenetrating 3D structure with large channel running through its net.