Recycling counter-current chromatography (CCC) together with step-gradient CCC and medium-pressure liquid chromatography (MPLC) was employed to separate nine anthraquinone compounds from Cassia obtusifolia L. in this study. The results showed that recycling CCC is a powerful tool for compounds that are difficult to separate with common elution mode. CCC was the better option for crude material while MPLC had advantage for the final tuning. The combination of recycling CCC and MPLC could simplify the method exploring process in the separation process. The structures of these compounds were identified according to their mass spectra, by (1)H-NMR and compared with standard compounds.