Two remarkable octamolybdates-based copper-organic complexes, namely, [Cu7(L)4(H2O)7(β-H2Mo8O26)]·7H2O (POM 1) and [Cu6(HX)4(β-Mo8O26)(H2O)6]·3H2O (POM 2) (H3L = 2-(pyridine-4-yl)-1H-imidazole-4,5-dicarboxylic acid; H3X = 2-(pyridine-3-yl)-1H-imidazole-4,5-dicarboxylic acid), were successfully assembled using two isomeric organic ligands under hydrothermal conditions. The two-dimensional metal-organic layers of POMs 1 and 2 were converted into three-dimensional frameworks by hexadentate β-H2Mo8O262− and tetradentate β-Mo8O264− clusters, respectively. The electrocatalytic properties of POM 1 were investigated, revealing its ability to catalyze the reduction of BrO3−, NO2− and H2O2 and the oxidation of ascorbic acid. Notably, POMs 1 and 2 demonstrated exceptional stability in organic solvents and exhibited excellent catalytic performance in oxidative desulfurization. When employed as catalysts for thioanisole oxidation, the conversion rates reached 94.5% after 150 min for POMs 1 and 99.9% after 120 min for POMs 2. In addition, their catalytic performances in model oil remained largely unchanged after five recycling cycles.