The invention relates to the technical field of organic small molecule isotope labeling, in particular to a stable isotope mercapto compound labeling reagent, a synthesis method and application thereof. The isotope labeling reagent is [d0] / [D4]-acridone-10-ethyl-N-maleimide. The reagent adopts acridone as the isotope group and takes maleimide as the reaction group. The synthesis method includes: taking [d0] / [D5]-bromobenzene as the raw material, and carrying out two-step condensation reaction, hydroxylation reaction, helogenation reaction, Gabriel reaction and acylation reaction, thus obtaining the reagent. The stable isotope deuterium label obtained by the invention is subjected to separation and purification, then the isotope labeling position is table, the chemical purity is up to 99.0% or more, and the isotope abundance is up to 99.0% or more. The reagent can selectively label mercapto compounds, and has the advantages of fast labeling reaction rate, high labeling yield and high mercapto selectivity, etc.