Phenolic 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-H2 O (1.5:2.5:1:5, v/v) [TFA (10 mM) was added in the upper phase and NH3 ·H2 O (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-H2 O (1:1, v/v) solvent system containing TFA (5 mM) and NH3 ·H2 O (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.