The invention provides a preparation method of a metal monatomic site catalyst. According to the synthetic strategy, a porous complex composite material coated with an acetylacetone metal salt is formed from a zinc compound and an imidazole organic ligand through coordination in a methanol solution of the acetylacetone metal salt, and then a porous carbon support doped with nonmetal heteroatomic nitrogen is formed from the imidazole organic ligand through a high-temperature pyrolytic reaction in an inert gas atmosphere, wherein metal atoms interact with surrounding nonmetal heteroatomic nitrogen and exist in the form of single atoms. The method is simple, safe, low in cost and applicable to synthesis of various noble metal and non-noble metal monatomic site catalysts, and the obtained metal monatomic site catalyst is high in metal concentration and good in heat stability, can be applied to the fields of energy, catalysis, medicine, biology and the like and has quite broad market prospect.