The invention provides a method for synthesizing a thiopyrimidone compound shown as a formula (III). The method includes: in an inertial atmosphere, adding a compound shown as a formula (I), a compound shown as a formula (II), a phase transfer catalyst, a cocatalyst and alkali into a solvent, adding an additive serving as a reaction promoter under a condition of stirring, performing reflux stirring reaction for 5-12h at 60-100 DEG C, filtering to remove the solvent after reaction is finished, performing silica gel column chromatography separation, collecting eluent, and removing elution solvent to obtain the compound shown as the formula (III) in the specification, wherein R1 and R2 are H, C1-C6 alkyl groups, C1-C6 alkoxy groups or halogen substituted C1-C6 alkyl groups respectively and independently, X refers to halogen, and n is an integer in a range of 1-6, R3 is halogen, an acyl group with 1-6 carbon atoms, an acyloxy group with 1-6 carbon atoms, a phenyl group, a substituted phenyl group or a substituted hexaceteroary group. By proper selection and combination of alkalis, solvents, catalysts and promoters, synergistic effects are achieved, high-yield high-purity products can be obtained, O-isomer generation is avoided, and the method has an extensive application potential in the field of nucleotide medical intermediate synthesis.