The invention provides a preparation method of a polymolybdophosphate-N-heterocyclic salt supramolecular compound. The method comprises the following steps: 1, weighing polymolybdophosphate and N-heterocycle; adding to reaction liquid; stirring to fully disperse; dropwise adding an acid conditioner to condition the pH of the reaction liquid to be 1.0-5.0; and continuously stirring until the reacting raw materials are completely dissolved; 2, sealing all reacting substances into a reaction kettle after the stirring is finished; heating and reacting until the reaction is finished; and cooling toobtain blocky crystals; and 3, post-processing the obtained blocky crystals to obtain the polymolybdophosphate-N-heterocyclic salt supramolecular compound. The method is simple in preparation processes, easy to obtain raw materials, low in cost, and high in yield.