The invention provides a comprehensive treatment method of three wastes of glyphosate, and relates to the field of waste disposal. According to the comprehensive treatment method, glyphosate mother liquor is concentrated, oxidized, cooled for precipitating phosphate and is subjected to membrane concentration and spray drying; the produced powdery solid is calcined together with methyl chloride waste gas, solvent recovery tail gas, methyl chloride and air; therefore, not only is the problem of treatment of the glyphosate mother liquor, methyl chloride waste gas and organic solvent waste gas solved, but also phosphate, sodium chloride and hydrochloric acid products are obtained. The produced hydrochloric acid is used for supplementing the glyphosate hydrolysis demand vacancy, and the water and concentrated liquid in the process are fully reused, so that cycle production is achieved, and the comprehensive utilization of the three wastes of the glyphosate is realized.