The development of an approach based on simultaneous supercritical fluid extraction-sample cleanup, followed by supercritical fluid chromatography/tandem mass spectrometry (SFE-SFC-MS/MS) was as a tool for the extraction, separation and characterization of indole alkaloids of Uncaria rhynchophylla. A two-step SFE method was designed. A mixture of the U. rhynchophylla sample and an adsorbent named C18SCX with the ratio of 1:1 (w/w) was placed into an extraction cell. The extraction temperature was 40 °C and the pressure was 25 Mpa. In the first step, 10 % EtOH as the co-solvent was used to extract for 60 min, which was considered as a cleanup process to remove non-alkaloid components. In the second step, 0.1 % DEA was added to 10 % EtOH and it extracted for 60 min to obtain the desired extract. By introducing an additional adsorbent, the specificity of SFE towards alkaloids was greatly improved. An SFC-MS/MS method was then utilized for analysis of the SFE extract. Using 2-EP as stationary phase with the gradient elution of 0–10 min, 5–25 % EtOH (+0.05 % DEA) in CO2, column temperature 40 °C, and back pressure 13.8 Mpa, 10 peaks were separated within 8 min. Further MS/MS analysis confirmed that nine of the 10 peaks in the SFE extract were indole alkaloids. This study developed a supercritical fluid-based method specifically towards extraction and analysis of alkaloids, which is helpful to the study of alkaline compounds in complex samples.