Materials with ordered mesoporous structures have shown great potential in a wide range of applications. In particular, the combination of mesoporosity, low dimensionality, and well-defined morphology in nanostructures may exhibit even more attractive features. However, the synthesis of such structures is still challenging in polar solvents. Herein, we report the preparation of ultrathin two-dimensional (2D) nanoflakes of transition-metal phosphates, including FePO4, Mn3(PO4)2, and Co3(PO4)2, with highly ordered mesoporous structures in a nonpolar solvent. The as-obtained nanoflakes with thicknesses of about 3.7 nm are constructed from a single layer of parallel-packed pore channels. These uniquely ordered mesoporous 2D nanostructures may originate from the 2D assembly of cylindrical micelles formed by the amphiphilic precursors in the nonpolar solvent. The 2D mesoporous FePO4 nanoflakes were used as the cathode for a lithium-ion battery, which exhibits excellent stability and high rate capabilities.