Foodborne illness and spoilage losses caused by microbial contamination or colonization are still major postharvest issues of horticultural produce. Simple treatments (such as washing and precooling) can only reduce microorganisms on the surface of produce and slow their growth. Chlorine dioxide (ClO2) that has been widely used in postharvest handling of fresh produce is a superior antimicrobial and preservative due to its broad-spectrum, efficient, green, and safe. However, the specific antimicrobial mechanisms and impacts on fresh produce need to be further elucidated. This paper reviews action mechanism of ClO2 based on its selective oxidation capacity, action sites, and intracellular interactions, particularly the antimicrobial effect and mechanism on different bacteria and fungi. Its antimicrobial effect is closely related to its action form (gaseous and aqueous), microbial species, treatment concentration and time. ClO2 first contacts the cell membrane wall, and then subsequently enters the cell to affect the internal components of the cell. Different biomolecules have different sensitivities to ClO2, both in vitro and in cells. We present some of the additional advantages that ClO2 shows in its postharvest application. For instance, ClO2 is able to stimulate plant innate immunity, preserve the quality characteristics of the commodity, remove hazardous factors, and as a potential controlled release agent in antimicrobial packaging. Overall, this study could provide useful information and new insights into the rational application of ClO2 for microbial safety.