RP-HPLC is the main method for the analysis of alkaloids. However, peak tailing is a problem that commonly occurs in the separation of alkaloids. In order to overcome this, three kinds of RP columns were compared for the analysis of protoberberine alkaloids in Coptidis Rhizoma and Phellodendri Cortex in this work. XTerra MS C18 column was the best one which gave the best symmetry factor under the same conditions. With this column, a good separation of the crude extracts of C. Rhizoma and P. Cortex was achieved using 0.1% v/v formic acid buffer and methanol as mobile phase. At the same time, the crude extracts of C. Rhizoma and P. Cortex were analyzed by the LC-ESI-MSn and LC-atmospheric pressure chemical ionization (APCI)-MSn methods. In the analysis of HPLC-ESI/MSn, structures of five protoberberine alkaloids were elucidated, compared to authentic standards, and data from the literature. At the same time, the structure of a novel compound was elucidated. In the HPLC-APCI/ MSn analysis, there was an interesting phenomenon that the relative abundance of the ions M+ and [M + 2]+ was different for different alkaloids. The possible fragmentation pathways of protoberberine alkaloids in APCI/MS analysis were studied for the first time in the present work.