Amphiphilic peptides are receiving considerable interest for drug delivery because of their self-assembly nature. A molecular dynamics simulation study is reported here to investigate the self-assembly of FA32 peptide composed of 32 amino acid (AF)6H5K15. The peptide, as well as water and counterions, are represented by the MARTINI coarse-grained model. Within 5 μs simulation duration, the peptide is observed to form micelles. Ala and Phe stay in the hydrophobic core, Lys in the hydrophilic shell, and amphiphilic His at the interface. The assembly process and microscopic structures are analyzed in terms of the number of clusters, the radii of micelle, core and shell, and the density profiles of residues. A three-step process is proposed for the assembly: small clusters are initially aggregated and then merged into large clusters, eventually micelles are formed. The effects of simulation box size and peptide concentration are examined in detail. It is found that the micellar structures and microscopic properties are essentially independent of box size. With increasing concentration, quasi-spherical micelles change to elongated shape and micelle size generally increases. The simulation study provides microscopic insight into the assembly process of FA32 peptide and the microscopic structures.