In this paper, a clean process for the synthesis of 4,6-dichloropyrimidine (DCP) was reported. Firstly, 4,6-dihydroxypyrimidine (DHP) was prepared from formamide (HCONH2), dimethyl malonate [CH2(COOCH3)2] and sodium methoxide (CH3ONa) as the catalyst. When the ratio was n[CH2(COOCH3)2]:n(HCONH2):n(CH3ONa) = 1:4:4, and the reaction temperature and time were 60 ℃ and 2 h, respectively, the yield of DHP could reach 90.4%. Then, DHP was reacted with phosphorus oxychloride (POCl3) at 60 ℃ for 2 h to obtain DCP, during this reaction process, 5-ethyl-2-methylpyridine was used as the acid binder, and 1,2-dichloroethane as the solvent. The optimal molar ratio of materials was n(DHP):n(POCl3):n(5-ethyl-2-methylpyridine) = 1:2.2:1.8, the yield of DCP was up to 94.5%. Finally, the chlorinated wastewater was treated with calcium hydroxide[Ca(OH)2] and the recovery rate of the acid binder is larger than 94%. The calcium phosphate[Ca3(PO4)2] can be effectively separated from the calcium chloride (CaCl2) solution, and the recycling of waste water in the DCP production process is realized. Therefore, the wastewater could be avoided successfully and the goal of clean production of DCP was achieved.