Toxin-antitoxin (TA) systems, widely existing in microorganisms, are composed of stable toxin and unstable homologous antitoxin, and participate in stress response and regulating microbial growth. The viable but non-culturable (VBNC) state is a dormant state that is developed by certain microorganisms in adverse environments. In the VBNC state, microorganisms cannot grow on conventional media. However, VBNC cells still have metabolic activity and can restore their culturability under appropriate conditions. Therefore, foodborne pathogens in the VBNC state can pose a potential threat to food safety and human health. In this article, we review recent studies on the relationship between TA systems and the formation of microbial VBNC state and propose possible mechanisms for the influence of TA systems on the formation of microbial VBNC state. Hopefully, this review will provide a reference for studies on the mechanisms of VBNC state formation.