Compared to commonly employed liquid chromatography-based methods, quantitative nuclear magnetic resonance (qNMR) is a recently developed method for accurate quantification of natural compounds in extracts. The simultaneous quantification of ellagitannins and the related polyphenols of Geranium thunbergii were studied using qNMR after a short-term and long-term decoction. The qNMR fingerprint for quantifying ellagitannin was presented in this work. Geraniin was observed in the short-term decoction as a major component while corilagin was the major component of the long-term decoction. An aqueous acetone extract of G. thunbergii after long-term decoction was extracted with diethyl ether, ethyl acetate, and n-butanol. Corilagin was found as a major constituent in the ethyl acetate and n-butanol extracts. Furthermore, the contents of these polyphenols in G. thunbergii from six locations in Japan and three locations in China were quantified. The contents of geraniin and corilagin in G. thunbergii from Japan were higher than those from China. Our finding raised the possibility that qNMR can be effectively employed as a simple, accurate, and efficient method for quantification of ellagitannins in medicinal plants.