Five Pd(II)/polyoxometalate catalysts with a unique atomic arrangement and high Pd loading were synthesized under solvothermal conditions, and their structures were determined by single crystal X-ray diffraction. The synergistic effect of polyoxometalate anions and Pd allows the Suzuki–Miyaura reactions to proceed under mild conditions. The structure of one of the five compounds can still be maintained without a significant yield decrease after four continuous reaction cycles. In order to further explore the versatility of this catalyst, 5-bromofuran-2-carbaldehyde, a furfural derivative, 3-bromo-7-(diethylamino)-2H-chromium-2-ketone, a fluorescent probe intermediate, and methyl(E)-3-(1-benzyl-6-bromo-1H–1H-indol-3-yl) acrylate, an indole anti-cancer drug intermediate, were synthesized.