The retention mechanism of a series of peptides on a single-wall carbon nanotube (SWCNT) stationary phase inside an HPLC column was investigated over a wide range of mobile phase compositions. While the similar size C18 column exhibited an efficiency of 11.5 μm, the SWCNT column increased the efficiency, i.e. 7.10 μm at a flow rate of 0.8 mL/min, and significantly affected the separation quality of the peptides. The values of enthalpy (ΔH) and entropy (ΔS(*)) of transfer of the peptides from the mobile to the SWCNT stationary phase were determined. The method studied each factor, i.e. ACN fraction x in the ACN/water mixture and column temperature. The changes in retention factor, ΔH and ΔS(*) as a function of the ACN fraction in the mobile phase were examined. These variations are explained using the organization of ACN in clusters in the ACN/water mixture and on the steric and electronic forces implied in the retention process. The information obtained in this work makes this SWCNT stationary phase useful for peptide research and demonstrated the role of ACN to improve the separation quality.