The invention relates to a clean production method for amino acids such as iminodiacetic acid. The method comprises the steps: carrying out alkaline hydrolysis on amino-nitrile by adopting cheap lime cream, and carrying out deamination, so as to obtain an iminodiacetic acid calcium salt crude product; suspending the obtained iminodiacetic acid calcium salt crude product into water or mother liquor, adding sulfuric acid or other inorganic acid into the water or mother liquor for acidification, and filtering out an inorganic calcium salt filter cake with low water solubility; and subjecting the filter liquor to cooling and crystallization, carrying out separation so as to obtain iminodiacetic acid solids, and applying the crystallization mother liquor to an acidification reaction of next batch mechanically. During the acidification by the sulfuric acid, gypsum can be converted into calcium carbonate and ammonium sulfate by further using a byproduct, i.e., ammonia water of an alkaline hydrolysis process and carbon dioxide in flue gas, so as to directly generate compound fertilizers; the calcium carbonate can also be separated, and ammonium sulfate crystals can also be concentrated; and the calcium carbonate can be sold as a byproduct or be subjected to heated decomposition so as to obtain a quicklime raw material which can be applied mechanically. According to the novel process, the complete utilization of resources can be realized, the reaction selectivity is higher, the production of colored byproducts is reduced, and a concentrating process for removing waste salts such as sodium sulfate and sodium chloride and a wastewater treatment link are avoided; and due to concentration, the use level of a decolorant can be greatly lowered, the energy saving and consumption lowering effects are remarkable, and the production cost is reduced remarkably.