2D-HPLC is an important technique for the separation of complex samples. Developing new types of stationary phases is of great interest to construct 2D-LC systems with high orthogonality. In this study, a novel stationary phase-Click dipeptide (l-phenylglycine dipeptide) was prepared by immobilization of alpha-azido l-phenylglycine dipeptide on alkyne-silica via click chemistry. In the preparation of this new material, an efficient, inexpensive and shelf-stable diazo transfer reagent (imidazole-1-sulfonyl azide hydrochloride) was utilized to transfer the amino group of l-phenylglycine to corresponding azido group under mild conditions. The Click dipeptide thus prepared was confirmed by FT-IR, solid state CP/MAS (13)C NMR and elemental analysis. The Click dipeptide packing showed high orthogonality with C18, which reached 63.5%. An off-line 2D-RP/RPLC system was developed to analyze a traditional Chinese medicine (TCM)-Rheum Palmatum L. The results showed high orthogonality between Click dipeptide and C18 as well as great separating power in the practical separation of complex samples.