The invention relates to a process for comprehensively treating a mother liquor containing sodium chloride, obtained by the synthesis of an IDA line n-(phosphonomethyl)iminodiacetic acid. The treatedsodium chloride meet the quality requirement for producing caustic soda by electrolysis, in particular, the concrete treatment steps comprises: an n-(phosphonomethyl)iminodiacetic acid, an n-(phosphonomethyl)iminodiacetic acid homolog and a dense liquid richly concentrated on the inner side of the film of the sodium filtration film condensed mother liquor are used to recover the n-(phosphonomethyl)iminodiacetic acid, and coarse sodium chloride is obtained by the dehydration crystallization of a weak liquor; the coarse sodium chloride is treated to obtain refined sodium chloride which can be directly used for producing caustic soda by electrolysis. By the comprehensive treatment method of the invention, the n-(phosphonomethyl)iminodiacetic acid of the n-(phosphonomethyl)iminodiacetic acid mother liquor can be effectively recovered, the by-product sodium chloride in the waste water can be fully utilized, thereby thoroughly meeting the requirements on economy, energy conservation and environmental protection.