With an aim to catalyze the synthesis of aspirin in a green approach, an unreported supramolecular compound [H3(C13H14N2)2][PMo12O40] (PMo12O40-Bpp) based on Keggin-type has been regarded as catalyst in synthesis of aspirin, which is prepared with flexible 1,3-bis(4-pyridyl)propane (C13H14N2, Bpp) and characterized structurally. Structural analysis of X-ray single crystal diffraction reveals that charge-assisted hydrogen bonds (CAHBs) N+-H…O- is formed between N+ of protonated Bpp molecule in PMo12O40-Bpp as hydrogen bond donor and molybdenum phosphate oxide cluster anion [PMo12O40]3-, and 3D supramolecular framework with porous is connected by intermolecular hydrogen bonds C9-H9…O3, C11-H11…O3 and C6-H6…O7 alternatively. When reactants of pharmaceutical esterification are salicylic acid and acetic anhydride, by screening dose of catalyst PMo12O40-Bpp, temperature and reaction time, the optimal conditions are determined as follows: 0.15 g PMo12O40-Bpp (mass fraction 5%), 90 °C and 55 min. Under these conditions, the yield of aspirin, the conversion rate of salycilic acid and the selectivity of catalyst can reach up to 69.24%, 98.02% and 70.64%, which indicating that catalytic activity is similar to that of concentrated sulfuric acid (85%) under the same reaction conditions. The kinetic results of pharmaceutical esterification of aspirin catalyzed by PMo12O40-Bpp show that reaction order is 1.37, rate constant is 1.13 × 10-3 k/L·(mol·s)-1, and apparent activation energy is 64.39 kJ·mol−1. After PMo12O40-Bpp catalyzes pharmaceutical esterification of aspirin repeatedly, PXRD, IR and lifetime of catalyst show that structure of PMo12O40-Bpp is unchanged and catalytic activity does not decrease significantly, indicating that PMo12O40-Bpp can be recycled for multiple times. Above experimental results may be due to specific “pseudo-liquid phase” phenomenon of POM-based supramolecular compounds to make full contact with reactants in the catalytic process, further stabilizing carbocation intermediates effectively through [PMo12O40]3- with greater surface electronegativity, which is more conducive to attack of hydroxyl oxygen atom on salicylic acid to promote pharmaceutical esterification reaction of aspirin catalyzed by PMo12O40-Bpp. This successful work implies that POM-based supramolecular compounds as catalysts in pharmaceutical synthetic process have potential to reduce environmental pollution and provide newfangled inspirations for green pharmaceutical chemistry.