A new porous organic–inorganic hybrid molybdenum phosphonate nanomaterial (HMoP‐1) was synthesized through the reaction of benzene‐1,3,5‐triphosphonic acid and molybdenum(V) chloride under hydrothermal conditions in the absence of any structure‐directing agent. The morphology of the hybrid material was found to be different at different synthesis temperatures. The material synthesized at 423 K (HMoP‐1‐LT) has spherical particle morphology, and the material synthesized at 453 K (HMoP‐1‐HT) has self‐assembled flakelike morphology. Powder XRD, field‐emission SEM, high‐resolution TEM, N2 sorption, solid‐state 13C cross‐polarization magic‐angle spinning NMR and 31P magic‐angle spinning NMR analyses, X‐ray photoelectron spectroscopy, thermogravimetric differential thermal analysis, NH3 temperature‐programmed adsorption, and FTIR spectroscopic techniques were employed to characterize the samples and understand the morphological diversity. The orthorhombic crystal phase of the material was established through REFLEX and CELSIZ unit cell refinement programs. The calculated unit cell parameters of HMoP‐1‐HT are a=8.001(0.046) Å b=7.029 (0.039) Å, c=6.010 (0.036) Å; whereas HMoP‐1‐LT is amorphous in nature. HMoP‐1‐HT shows outstanding catalytic activity and high recycling efficiency for the green and efficient one‐pot condensation reaction for the synthesis of bioactive 2‐aryl benzimidazoles in excellent yields at room temperature.