Abstract: The non-covalent interaction between a series of N-diisopropylphosphoryl dipeptides(or methyl esters) (DPP) and amino acids was studied by ESI-MS. The results show that aromatic rings to form π–π conjugated system could greatly strengthen the interaction. Also, the polar groups generating hydrogen bonds are favourable to the complexes. In addition, the molecule size, flexibility and steric hindrance show obvious effects on the interaction. While, the chirality of amino acids has no effect on the interaction between DPP and amino acids under ESI-MS conditions.