Antibacterial peptides (ABP) are a new type of antimicrobial substance. It is widely distributed in many living organisms, from the lowest virus and germs to the higher propagation. The research foregone mostly focused on the mechanism of ABP against the cell membrane, and three modes have been put forward. Recent researches indicate that many antibacterial peptides can penetrate into the bacterial cell effectively. They act on biologic molecules inside bacterium directly without disruption of the membrane. According to different structure of antibacterial peptides, there are several mechanisms to penetrating through the membrane. By interacting with nucleic acids, proteins and signal transmissions, antibacterial peptides can finally kill and wound bacterium.