The invention discloses a method for performing two-phase recognizing, fractionating, extracting and separating on pantoprazole sodium enantiomer. The method takes hydroxypropyl-beta-cyclodextrin and D-isobutyl ester tartrate as extracting agents, utilizes centrifugal acting force of a centrifugal extractor to strengthen mass transfer efficiency, and accelerate mass transfer and reaction of pantoprazole sodium enantiomer in a water phase and an organic phase. The method disclosed by the invention is utilized, so that quick and high-selectivity separation of pantoprazole sodium is realized by virtue of multi-stage counter-current extraction. And moreover, equipment is simple, operation is simple and convenient, and the cost is low.