The invention provides a preparing and refining method of S-pantoprazole sodium. According to the method, 5-difluoromethoxy-2-[[(3,4-dimethoxy-2-pyridyl)methyl]sulphur]-1H-benzimidazole is subjected to an oxidation reaction with cumene hydroperoxide, which is a mild oxidizing reagent, under the catalysis of a system consisting of tetraisopropyl titanate, D-(-)-diethyl tartrate and N,N-diisopropyl ethylamine, and S-(-)-5-difluoromethoxy-2-[[(3,4-dimethoxy-2-pyridyl)methyl]sulfinyl]-1H-benzimidazole, namely S-pantoprazole sodium, is obtained; and then, through an in-situ sodium salt forming reaction and recrystallization refining, high-purity S-pantoprazole sodium is obtained. The preparing method has the advantages of simplicity, low cost, high yield and mild reaction conditions, thereby being ideal for industrial production of S-pantoprazole sodium.