Salvia miltiorrhiza Bunge (S. miltiorrhiza), also known as red sage, has been traditionally used to prevent and treat cardiovascular and cerebrovascular diseases. Tanshinone IIA (TIIA) and cryptotanshinone (CT) are major active compounds isolated from the root of S. miltiorrhiza, which are effective against inflammation, cancer, fibrosis, apoptosis, oxidative stress and cardiovascular diseases. The aim of this study was the quantitative analysis and purification of TIIA and CT in ethanol extract and fractions from S. miltiorrhiza root. S. miltiorrhiza was extracted with 100% ethanol by the immersion method. And S. miltiorrhiza extract (SME) was fractionated with n-hexane, dimethyl chloride, ethyl acetate and n-butanol. Among fractions, the hexane fraction was separated on a macroporous resin column. The validated HPLC method was utilized to analyze the contents of TIIA and CT in SME and fractions. The contents of TIIA and CT in SME were 7.28 and 4.62%. The contents of TIIA and CT were the highest in the hexane fraction at 8.53 and 15.33%, respectively. After resin column, the content of TIIA was increased to 4.85 times (from 8.53 to 41.38%) in 100% ethanol fraction of the third sub-fraction, and the content of CT was increased to 3.13 times (from 15.33 to 47.95%) in 90% ethanol fraction of the second sub-fraction. The result of this study may be used for the basic data for developing functional foods or medicinal products from S. miltiorrhiza.