The invention belongs to the field of chemical synthesis and provides a novel method of preparing N-phosphonomethyl iminodiacetic acid. The method comprises the following steps: adding iminodiacetonitrile and an inorganic acid into a reaction kettle, and mixing and carrying out acidolysis; then adding water and iminodiacetic acid application liquid; carrying out alkalization by using concentrated ammonia water with the mass percent of 25-28%, and adjusting the pH to be 1-3; cooling, filtering and crystallizing to obtain iminodiacetic acid; mixing the iminodiacetic acid, hydrochloric acid and phosphorous acid, and dropping a formaldehyde solution with the mass percent which is more than or equal to 37% to carry out a condensation reaction to obtain the N-phosphonomethyl iminodiacetic acid. According to the method provided by the invention, the iminodiacetic acid application liquid can be repeatedly applied to a preparation process of the iminodiacetic acid; N-phosphonomethyl iminodiacetic acid application liquid also can be applied for more than 10 times and not much wastewater is produced in a whole production process; meanwhile, active carbon solid wastes used for de-coloring treatment are obviously reduced; the substances of the phosphorous acid, the hydrochloric acid and the like are repeatedly applied to the reaction in an N-phosphonomethyl iminodiacetic acid mother solution and the salt amount and the phosphorus amount finally reach the emission standards, so that a large-size wastewater treatment device does not need to be mounted and the production cost is greatly saved.