A botanical injection is a special drug preparation with extremely high safety requirements. Therefore, many separation technologies, such as ethanol precipitation and liquid liquid extraction, are applied in the manufacturing process of botanical injections to purify efficacy compounds and remove impurities. In this work, second ethanol precipitation and 1-butanol extraction were compared in the purification of the concentrated supernatant of danshen (the dried root of Salvia miltiorrhiza). These two separation technologies showed satisfactory recovery of phenolic compounds and similar removal of total protein. Liquid-liquid extraction removed more saccharides than second ethanol precipitation. Accordingly, the purity of phenolic compounds increased remarkably after liquid-liquid extraction. According to the characteristics of the two separation technologies, the combination technology of "ethanol precipitation + liquid liquid extraction" showed more advantages in drug safety and product quality control than the combination technology of "ethanol precipitation + second ethanol precipitation".