The invention provides a clean preparation method of 1, 8-dinitro-3, 6-naphthalenedisulfonic acid. A reaction formula is shown in the description. The method includes: taking 2, 7-naphthalenedisulfonic acid as a reaction raw material, adopting sulfuric acid as a solvent, and adding fuming nitric acid with a content of 98% dropwisely to prepare 1, 8-dinitro-3, 6-naphthalenedisulfonic acid; and after the end of the reaction, adding water to conduct dilution and isolating the product, subjecting the remaining nitrification mother solution to flocculation treatment so as to remove impurities, and then carrying out pressure reduction concentrating to recover the sulfuric acid as the solvent for next reaction. The method provided in the invention has the advantages of short technological process, simple operation, good quality product, and no wastewater discharge, thus being suitable for industrialized production.