To understand the details of the permeation pathways of antimicrobial peptide JCpep8, the antimicrobial processes were investigated step by step in this paper. First, the characterization of the initial binding process was explored by introducing the living Staphylococcus aureus cells (LSACs) into electrophoretic buffer used as pseudo-stationary phase in capillary electrochromatography (CEC), and the thermodynamic parameters were determined. The binding constants at 298, 303, and 309 K were 7.40 × 10¹¹, 1.43 × 10¹², and 2.6 × 10¹² M⁻¹, respectively, which indicated the evident interaction between JCpep8 and LSACs. This binding process was spontaneous. Both the electrostatic force and hydrophobic effect play major roles in this binding process. Second, antibacterial activity kinetics and outer membrane and inner membrane disruption assays were investigated. Data indicated that JCpep8 killed microbes principally by breaking their cell wall and membrane, followed by cell lysis. The results were confirmed by Fourier transform infrared (FTIR) spectroscopy and transmission electron microscopy (TEM). In summary, JCpep8 kills microbes mainly by wall-/membrane-targeting pore-forming mechanisms.