In this study, a special orthogonal separation method, named as dual-tautomerism separation (DTS), was developed for the purification of tautomeric compounds from complex matrixes. In DTS, isomers of these compounds are individually collected and asymmetrically transformed to the mixtures of isomers. After separating the mixture with an identical method, high-purity compounds can be prepared from the newly generated isomers but impurities remain in another one. To validate the effectiveness, a DTS was developed to prepare punicalagin in gram-scale from pomegranate peel waste. Isomerization kinetic and thermodynamic of punicalagin were accurately assayed by dynamic HPLC built on low-temperature or/and loop-based stop-flow two-dimensional liquid chromatography. After the isomerization based on it, 9.3 g of pomegranate peel extract was firstly separated on C18 column, and F-alpha and F-beta around alpha-punicalagin and beta-punicalagin were obtained. Then, the proportion of alpha-punicalagin in F-alpha and F-beta was optimized to 52.7% and 32.0% based on isomerization kinetics and thermodynamic. With the aid of low-temperature injection, F-alpha and F-beta were loaded and secondly purified. After waste recycling, totally 3.0 g of punicalagin with the purify of 99.5% was obtained within two days, which would strongly support the resource utilization of pomegranate peel waste. Because only an individual method was employed in the two-step purification, the separation in DTS was fully compatible.