Lipid A is the major component of lipopolysaccharide, which forms the outer monolayer of the outer membrane in most Gram-negative bacteria. Lipid A is responsible for the bioactivity of endotoxin. After entering the host, lipid A can be recognized by immune cells, which may lead to diseases. The biosynthetic pathway of lipid A in bacteria is relatively conservative, but structure modifications can occur during its transport to the bacterial surface. These modifications differ in bacteria in order to adapt to different external environment. They are not necessary for survival, but are tightly regulated in the cell and closely related to the virulence of bacteria. This review summarizes recent advances on the modification of lipid A and its relationship with the virulence of bacteria. Furthermore, applications of such research in pathogen control, vaccine development, and fermentation industry are proposed.