An effective method utilizing the same RP chromatographic column with different pH in first and second LC dimensions has been developed for separation of the basic compounds from traditional Chinese medicines (TCMs). In this work, the alkaloids in Corydalis yanhusuo which is an important TCM were selected as a model to develop the method. The additives and pH values of the mobile phase were optimized in this work. To investigate the feasibility of this method, off-line mode separation was performed in the experiments. According to the UV-absorption intensity, there were eight fractions collected in acidic conditions. All the fractions were analyzed in basic conditions. The results showed that the chromatographic selectivities were significantly different in the separations performed with acidic and alkaline elution systems. Complementary separation was achieved in this work. It is demonstrated that this method would be an effective tool for alkaloids research. Based on the different pH of the mobile phase in this method, it could also be suitable to analyze compounds which were sensible to the pH of the solution.