Here we report a novel family of crystalline, supermicroporous iron(III) phosphonate nanomaterials (HFeP‐1‐3, HFeP‐1‐2, and HFeP‐1‐4) with different FeIII‐to‐organophosphonate ligand mole ratios. The materials were synthesized by using a hydrothermal reaction between benzene‐1,3,5‐triphosphonic acid and iron(III) chloride under acidic conditions (pH≈4.0). Powder X‐ray diffraction, N2 sorption, transmission and scanning electron microscopy (TEM and SEM) image analysis, thermogravimetric and differential thermal analysis (TGA‐DTA), and FTIR spectroscopic tools were used to characterize the materials. The triclinic crystal phase [P$\bar 1$(2) space group] of the hybrid iron phosphonate was established by a Rietveld refinement of the PXRD analysis of HFeP‐1‐3 by using the MAUD program. The unit cell parameters are a=8.749(1), b=8.578(1), c=17.725(3) Å; α=104.47(3), β=97.64(1), γ=113.56(3)°; and V=1013.41 Å3. With these crystal parameters, we proposed an 24‐membered‐ring open framework structure for HFeP‐1. Compound HFeP‐1‐3, with an starting Fe/ligand molar ratio of 3.0, shows the highest Brunauer–Emmett–Telller (BET) surface area of 556 m2g−1 and uniform supermicropores of approximately 1.1 nm. The acidic surface of the porous iron(III) phosphonate nanoparticles was used in a highly efficient and recyclable catalytic transesterification reaction for the synthesis of biofuels under mild reaction conditions.