Two novel 3-D hybrid supramolecular isomers, namely, α-[Cu 2 (ABPT) 2 (H 2 O) 2 (Mo 8 O 26 )] n (1) and β-[Cu 2 (ABPT) 2 (H 2 O) 2 (Mo 8 O 26 )] n ·4nH 2 O (2), have been successfully isolated from one-pot hydrothermal crystallization and characterized. Single-crystal X-ray diffractions show that the ABPT ligands in compound 1 taking the transoid-configuration to link distorted octahedral copper centers into 1-D metal–organic chains, which are further interlaced by [Cu 2 (γ-Mo 8 O 26 )] inorganic ladder-like chains to generate a 3-D hybrid structure. In 2, the square-pyramidal Cu II centers are firstly linked by cisoid-ABPT ligands to give 2-D metal–organic coordination layers, which are connected by [δ-Mo 8 O 26 ] 4− clusters into a 3-D hybrid network. Compounds 1 and 2 both can be regarded as 3,4-connected nets based on nonequivalent nodes with (4 3 .6.8 6 ) 2 (4 2 .6) 2 (4 2 .8 4 ) and (4.8 2 ) 2 (4.8 2 .10 3 ) 2 topologies, respectively. By careful inspection of the structures of 1 and 2, it is believed that the ligand configuration plays a crucial role for the formation of these two hybrid supramolecular isomers.