In this report, a series of peptide nucleic acid amphiphiles (PNAAs) with hybridization properties were designed and synthesized. Driven by hydrophobic interaction, the hybridized PNAAs can form uniform micelles, the base stacking interaction from PNA segments further stabilized the micelles. The effects of hydrophobic alkyl chain length, structure of hydrophilic peptides, concentration, and pH on the self-assembly behavior of partly complementing PNAA duplexes were explored.