The first POMos-based hybrid with penta-coordinated Mo in trigonal bipyramid geometry for Mo–O clusters has been hydrothermally synthesized and characterized by IR, TG, XPS, and X-ray diffraction analysis. Structure analysis indicated penta-coordinated together with tetra-coordinated Mo existed in the POMos-based hybrid. The hybrid was successfully used as an efficient precursor for a hydrodesulfurization (HDS) catalyst for the first time.