The invention provides a post-treatment method for 4,6-dihydroxypyrimidine synthesis, belongs to the technical field of organic chemical industry, and relates to a method for alkali recovery and application and wastewater recovery and application in a chemical industry product, particularly to a process. According to the process, formamide, dimethyl malonate and sodium methoxide are adopted as starting raw materials and cyclization is performed to prepare 4,6-dihydroxypyrimidine; after the reaction is completed, negative pressure suction filtration is performed, the filtrate is subjected to partial methanol removing, and the alkali is recovered and applied; and after the filter cake is subjected to acidification crystallization, negative pressure suction filtration is performed, the filter cake is dried to obtain the product, the mother liquor is concentrated to recover the 4,6-dihydroxypyrimidine, and the acid water is neutralized so as to be recycled while the by-product salt can be recovered so as to be comprehensively utilized. According to the present invention, after the alkali recovery and application, the acid consumption for the subsequent acidification treatment can be significantly reduced so as to substantially reduce the production cost and the three-waste amount; and the post-treatment method has characteristics of less equipment investment, three-waste treatment cost reducing, easy raw material recovery and application, and the like, and is suitable for industrial production.