During the development of multifunctional and advanced energy materials, mesoporous organic-inorganic metal phosphonate hybrids are considered as a promising candidate for environmentally friendly materials with multifunctionalities, which have attracted much attention because of the combination of superior properties from both the organic and inorganic components. They are not just physical mixtures of organic and inorganic moieties, but regarded as nanocomposites with organic and inorganic components that are intimately mixed on a molecular level. By using organically bridged polyphosphonic acids and their derivatives (i.e. salts and esters) as coupling molecules, the homogeneous incorporation of a considerable number of organic functional groups into the hybrid framework has been realized. Furthermore, the incorporation of mesoporosity with high surface area, adjustable pore size and large pore volume could contribute to the enhanced performances in various areas. This paper systematically reviewed the synthesis principle of the mesoporous metal phosphonates including the synthesis mechanism, mesophase adjustment, pore size control, morphological design and the crystallinity enhancement. The applications of these materials in the fields of adsorption, separation, catalysis, biosensing and controlled drug release were elaborated and the further development and the perspective of the mesoporous phosphonate were expected.