This paper describes an improved quality assessment method for Radix Salviae Miltiorrhizae (Root of Salvia miltiorrhiza BGE.) which was established using chromatographic fingerprinting and quantification of multiple marker compounds in the crude drug. High-performance thin-layer chromatography (HPTLC) fingerprinting of water-soluble phenolics and nonpolar tanshinones was performed separately and the authentication of Radix Salviae Miltiorrhizae was achieved by comparing the fingerprints of the samples with those of the reference crude drug and by comparing the Rf values of the bands in TLC fingerprints with those of reference compounds. HPLC fingerprints were obtained by simultaneous separation of phenolics and diterpenoids in Radix Salviae Miltiorrhizae. The HPLC fingerprints of seven batches of samples from different regions of China showed similar chromatographic patterns, and seven peaks were selected as characteristic peaks. The relative retention time of these characteristic peaks in the HPLC fingerprints was established as an important parameter for the identification of this herbal medicine. The pharmacologically active marker compounds salvianolic acid B, rosmarinic acid, and tanshinone IIA in herbal medicine were quantitatively determined using reverse-phase HPLC techniques. The HPLC quantitation methods of the three marker compounds were validated and the measurement uncertainty, which is important for setting the proposed content limit of the marker compounds in herbal medicine, were further evaluated.