The invention discloses a method of controlling harmful impurities during pirimiphos-methyl synthesis. The method includes following steps: adding 2-N, N-diethylamino-6-methyl-4-hydroxy pyrimidine metal salt and a catalyst into an organic solvent; dropwise adding O, O-dimethyl thiophosphoryl chloride for condensation reaction; after-treating obtained reaction liquid to obtain pirimiphos-methyl to complete control on harmful impurities. By the method, content of the harmful impurities can be controlled effectively, and amounts of the harmful impurities like methyl sulfotepp (<0.06%) and iso-pirimiphos-methyl (<0.2%) are far lower than FAO limited concentration standards.