The invention discloses a synthesizing method of a single-configuration rabeprazole metabolite.According to the method, rabeprazole thioether serves as a starting material, and the rabeprazole metabolite is synthesized through a five-step reaction.The optimal preparation steps and reaction conditions are screened out through a large number of experiments, the whole technological design is reasonable, and the operability is high.According to the obtained single-configuration rabeprazole metabolite, the chemical purity can reach 99% or above, and the chiral purity is larger than 99.5%.The obtained single-configuration rabeprazole metabolite provides a standard substance for metabolic mechanism research of a rabeprazole drug, can be used for exploring the metabolic process of the drug in organisms and has a great application research value in clinical pharmacokinetic research.