In recent years, heavy metal contamination in China has greatly increased due to the discharge of industrial wastewater and daily human activities. People living in polluted areas suffer from serious health problems as a result of long-term ingestion of contaminated crops. Therefore, it is of utmost importance to repair heavy metal pollution in developing countries. Recent studies have mainly focused on the probiotics effectively combine with heavy metals in vitro and in vivo, and different mechanisms have been proposed to explain the functions of probiotics in heavy metals’ remediation. In view of the current situation, heavy metals such as cadmium, lead, and chromium have serious impacts on the environment and animal health, this review analyzes the sources of heavy metals pollution and the control of various heavy metals in the environment and animal intestines. Meanwhile, the mechanisms of heavy metal remediation processes by probiotics are summarized, and the utilization of probiotics in alleviating heavy metals’ toxicity on human and the environment in the future.