Human activities, especially industrial production, have aggravated the pollution of heavy metals in the environment, and especially after disrupting the food chain, such pollution can cause varying degrees of heavy metal poisoning in human beings. Studies have shown that exposure to heavy metals tends to upset the balance of the flora and further aggravate organ toxicity. Intestinal probiotics represented by Lactobacillus can actively adsorb heavy metal ions, promote their excretion, and reduce their induced oxidative stress injury and inflammatory response. Focusing on the chronic toxicity induced by long-term low-dose exposure to heavy metals, this article reviewed current pollution status of several common heavy metals (lead, cadmium, and mercury), analyzed the interaction between heavy metals, intestinal flora, and probiotics, and summarized proposed mechanisms of probiotics in mitigating chronic heavy metal toxicity, aiming to provide new ideas for effective prevention and treatment of organ toxicity induced by heavy metals.