Nowadays, chromatographic methods are widely applied in contemporary chemistry, e.g.HPLC, HPLC–MS, etc. However, organic solvents are required here, sometimes even in large quantities, including toxic acetonitrile, methanol, etc. Hence, chemical methods with less or no use of organic solvents, the so-called green chemistry methods are attracting great interest. In this paper, a green micellar liquid chromatography (MLC) method is proposed, and the use of a micellar mobile phase to give a more sensitive and rapid separation than in conventional high-performance liquid chromatography (HPLC). As an example, the method was successfully applied to the analysis of cryptotanshinone (CT) and tanshinone IIA (TS), which are usually used as the bioactive markers in biological samples or herbal medicinal preparations. No extraction step is required. A C18 column and a micellar mobile phase of 0.15 M sodium dodecyl sulfate (SDS) and 6.4% n-butanol were used. No interferences were caused by proteins or endogenous compounds in the urine, serum samples and herbal medicinal preparations. The limits of detection (LODs) for CT and TS were 12.5 and 15 ng mL−1 in micellar solutions, 18 and 25 ng mL−1 in urine samples and 20 and 30 ng mL−1 in serum samples, respectively. Compared with conventional reversed-phase chromatography where methanol–water (75 : 25, v/v) is used as the mobile phase, the proposed MLC method is more sensitive and time-saving.