This paper reviewed the antibacterial activity and structure-activity relationship of isoquinoline alkaloids, such as protoberberine, protopine, benzophenanthridine, aporphine, double benzyl isoquinoline, etc. The antibacterial mechanism of alkaloids were illustrated from cell wall and membrane damage, membrane permeability changes, related enzymes and efflux pump inhibition, influence of bacterial DNA and related protein synthesis and so on. In addition, this paper summarized the structure-activity relationship of isoquinoline alkaloids. In order to improve the screening efficiency of drug targets, the complementary effect of biological information science and combinatorial chemistry should be developed abundantly in the development of natural product. This paper will provide a theoretical reference for the research and development of new antibacterial agent.