Provided is a determination method of formaldehyde-DNA adducts in saliva, namely the determination method of HOMe-dA and HOMe-dG in the saliva; the determination method includes the steps: collecting the saliva by using an OG-500 saliva collection tube, carrying out DNA extraction on the saliva, carrying out enzyme hydrolysis of the DNA solution, and successively adding a stable isotope internal standard, a reducing agent NaBH3CN and a DNA hydrolase; and carrying out solid-phase extraction of the hydrolysate with a Strata-X small column, collecting an eluted liquid, nitrogen-blowing to be dried at room temperature, redissolving in a methanol aqueous solution, introducing into an LC-MS/MS system, analyzing, and accurately detecting the content levels of Me-DA and Me-dG. The stable isotope is used as an internal standard quantitative analysis material, so the error caused by the sample pretreatment process can be reduced, and the selectivity, accuracy and sensitivity of the method can be improved by tandem mass spectrometry. Through selection and optimization of the chromatographic column and the elution conditions, the chromatographic separation process is relatively improved, the time of chromatographic analysis is shortened, and the consumption amount of an organic solvent is decreased.