An investigation into the molecular tectonics of metal–organic frameworks (MOFs) is reported on the basis of N-donor ligand modulated polynuclear zinc clusters and different aromatic polycarboxylic ligands. A series of three-dimensional (3D) coordination frameworks, [Zn2(BDC)1.5(L)(OH)]·H2O (1), [Zn2(BOABA)(L)(OH)]·2H2O (2), [Zn2(BOABA)(L)(OH)]·4H2O (3), [Zn3(BTC)2(OH)]·0.25H2O·[N(C4H9)4] (4) and [Zn2(BTEC)0.5(L)(OH)2] (5), were synthesized by self-assembly of zinc ions with a new N-donor ligand 4,5-diazafluoren-9-oxime (L) and the aromatic polycarboxylic ligands 1,4-benzenedicarboxylic acid (H2BDC), 3,5-bis-oxyacetate-benzoic acid (H3BOABA), 1,3,5-benzenetricarboxylic acid (H3BTC), and 1,2,4,5-benzenetetracarboxylic acid (H4BTEC). Compound 1 exhibits a twofold interpenetrated α-polonium-type network based on tetranuclear Zn clusters as six-connected vertices and BDC ligands as linkers. Compound 2 also consists of tetranuclear units, it shows a (3,6)-connected rutile network, where tetranuclear zinc clusters act as six-connected nodes and BOABA ligands act as three-connected nodes. Compound 3 is an isomer of compound 2, due to the different configuration of tetranuclear zinc, it displays a novel (3,6)-connected network with a complex (4·62)2(42·69·84) topology. In 4, the connection between the trinuclear zinc clusters and the BTC ligands results in an infinite 3D (3,6)-connected network with point symbol (4·62)(63)(4·611·83). Compound 5 constitutes a lvt net, which is built from tetranuclear clusters and BTEC as four-connected nodes, respectively. The results indicate that various polynuclear zinc clusters are modulated by L ligands combining with Zn atoms via chelation or monodentate coordination, or acting as a structure-directing agent. Meanwhile, aromatic multicarboxylic acids also play important roles in the construction of the compounds with various structures.