Caesalpinia sappan L. (C. sappan L.), a traditional Chinese medicine, has been widely used to treat bruises and dysmenorrhea, performing pharmacological activities such as anti-inflammatory and anti-tumor. C. sappan L. has been reported to contain compounds such as protosappanins, brazilins, and homoisoflavones. In the pre-experiments, we discovered that there were many unstable components in the characteristic chromatogram of C. sappan L. Here, silica-gel column chromatography, high-speed counter-current chromatography, and preparative high-performance liquid chromatography were combined and applied to isolate the unstable components from alcohol extract of C. sappan L. The results showed that four unstable compounds were collected with the purity higher than 95.0%, characterized as episapponal, brazilin, sapponal, and 4-O-methylsapponal by hydrogen-1 and carbon-13 nuclear magnetic resonance. Based on the above results, the characteristic chromatogram of C. sappan L. was established, and the characteristic peaks were identified. These results provided a theoretical basis for the quality assessment of C. sappan L.