A comprehensive two-dimensional (2D) reverse phase (RP) liquid chromatography (LC) method is developed for alkaloid analysis. This offline comprehensive 2D method is developed using different pH values. With a pH value of 10.5, most alkaloids appear in the form of neutral molecules possessing high retention factors based on their polarity, while the alkaloid polarity order is changed when the pH value decreased to 3.0. The performance of pH modulated 2D LC is demonstrated with 8 alkaloid standards which resulted in orthogonal separation. The developed method is then applied to total alkaloid separation in Corydalis yanhusuo. The first-dimension separation is carried out using methanol and water containing 1.0% ammonium hydroxide and a strong base-resistant RP column, which afforded a peak capacity of 94. The second-dimension analysis is carried out with a surface positive charge column providing a peak capacity of 205 using a mobile phase consisting of acetonitrile and water with 0.15% formic acid. 2D analyses of total alkaloid extract from C. yanhusuo afford a total peak capacity of 9090. Sixteen compounds were tentatively identified based on their ultraviolet spectrum and MS/MS analyses. The proposed method provides an alternative approach to achieve high peak capacity for analysis of alkaloid extract.