Wolbachia is a common group of intracellular bacteria in arthropods. They can alter host biology in diverse ways, including the induction of reproductive manipulations, such as feminization, thelytoky, male killing, and cytoplasmic incompatibility (CI). Among them, CI, the most common phenotype, refers to the fact that embryonic lethality occurs when a Wolbachia -infected male insect mates with a Wolbachia -uninfected or incompatible female insect, whereas the cross between the male and female both infected with the same strain of Wolbachia is compatible. CI is caused by linked pairs of Wolbachia genes known as CI factors (CifA and CifB). CifB as a toxin can induce CI in male insects, while CifA as an antidote can rescue CI in female insects. This review summarized the research on the structure, function, and mechanism of CI factors, aiming to provide a solid base for the future application of Wolbachia and CI in the prevention and control of mosquito-borne diseases and agricultural pests.