Ordered, hexagonal, mesoporous metal (Ti, Zr, V, Al)-phosphonate materials with microporous crystalline walls are synthesized through a microwave-assisted procedure by using triblock copolymer F127 as the template. Corresponding metal chlorides and ethylene diamine tetra(methylene phosphonic acid) are chosen as the inorganic precursors and the coupling molecule, respectively. X-ray diffractometry, transmission electron microscopy, N2 sorption, and thermogravimetry measurements confirm that the obtained metal phosphonates possess a hierarchically porous structure with pore sizes of 7.1–7.5 nm and 1.3–1.7 nm for mesopores and micropores, respectively, and the metal phosphonate materials are thermally stable up to around 450 °C with the pore structure and hybrid framework well preserved. Magic angle spinning NMR, Fourier-transform infrared spectroscopy, and X-ray photoelectron spectroscopy analyses indicate that the phosphonate groups are homogenously incorporated into the hybrid framework of the obtained materials. For the first time, the mesoporous hybrid materials are employed as the stationary phase in open tubular capillary electrochromatography technique for the separation of various substances including acidic, basic, and neutral compounds. These materials show good selectivity and reproducibility for this application.