A series of functional cation-regulated isopolymolybdate-based organic-inorganic hybrid compounds, Na2H2[Mo4O12(C8H17O5N)2]·10H2O (1), Na2[M(Bis-tris)(H2O)]2[Mo7O24]·10H2O [M = Cu, 2; Ni, 3; Co, 4; Zn, 5; Bis-tris = 2,2-Bis(hydroxymethyl)-2,2',2″-nitrilotriethanol], and (NH4)2[M(Bis-tris)(H2O)]2[Mo7O24]·6H2O (M = Zn, 6; Cu, 7), were synthesized and characterized toward advanced molecular catalyst design. Compound 1 is a covalently bonded adduct, and its self-assembly process can be probed by electrospray ionization mass spectrometry (ESI-MS). Compounds 2-7 are polyoxometalate (POM)-based hybrids containing classic heptamolybdate anions and complex cations with Bis-tris ligands. All of these compounds showed remarkable catalytic effects for selective sulfide oxidation. To the best of our knowledge, compound 5 presents the best catalytic activity so far among the reported hybrid materials with common easily synthesized small-molecule POM clusters and also exhibits outstanding reliability. The conclusion of the catalytic effect is drawn from the results that Zn-based compounds have better catalytic effects than other transition-metal-containing compounds and the compound constructed by Na+ has higher catalytic activity than that constructed by NH4+. The mechanism studies show that the improvements of the catalytic performance are caused by the synergy between classic heptamolybdate anions and complex cations. ESI-MS data and UV-vis spectra revealed that the POM anions can form intermediate peroxomolybdenum units during catalytic reaction. Further, the combination of the substrate thioanisole with complex cations was characterized by NMR experiments and UV-vis spectra. Thus, a new synergistic mechanism of anions and cations is proposed in which the activated thioanisole is used as a nucleophile to attack the peroxomolybdenum bonds, and this provides a new strategy in the design of reliable POM-based catalysts.