AbstractPhenolic acids are the main active components in Salvia yunnanensis Radix, which have significant effects such as cardiovascular protection, anti‐thrombosis, anti‐oxidant, and anti‐inflammation. In this study, pH‐zone‐refining counter‐current chromatography (pH‐ZRCCC) was successfully applied to the preparative separation of phenolic acids from S. yunnanensis Radix. First, a two‐phase solvent system composed of Pet–EtOAc–ACN–H2O (1.5:2.5:1:5, v/v) [TFA (10 mM) was added in the upper phase and NH3·H2O (30 mM) was added in the lower phase] was used for the separation of 4.0 g of the crude sample to obtain 55.6 mg of rosmarinic acid (1), 69.0 mg of caffeic acid (2), 18.9 mg of protocatechualdehyde (3), 14.6 mg of 8‐epiblechnic acid 9‐methyl ester (4), and a mixture containing two compounds. After the recovery, 1.3 g of the mixture was obtained and separated using the MtBE–H2O (1:1, v/v) solvent system containing TFA (5 mM) and NH3·H2O (60 mM) to obtain 259.9 mg of salvianolic acid B (5) and 28.75 mg of lithospermic acid (6). Moreover, a systematic separation pattern for separating the relatively low‐polarity phenolic acids from natural products by pH‐ZRCCC was summarized for the first time. This study provided technical support for the pharmacological activity and quality control research of S. yunnanensis Radix.