Polybrominated diphenyl ethers (PBDEs) are a group of flame retardants used in plastics, textiles, polyurethane foam, and other materials. They contain two halogenated aromatic rings bonded by an ester bond and are classified according to the number and position of bromine atoms. Due to their widespread use, PBDEs have been detected in soil, air, water, dust, and animal tissues. Besides, PBDEs have been found in various tissues, including liver, kidney, adipose, brain, breast milk and plasma. The continued accumulation of PBDEs has raised concerns about their potential toxicity, including hepatotoxicity, kidney toxicity, gut toxicity, thyroid toxicity, embryotoxicity, reproductive toxicity, neurotoxicity, and immunotoxicity. Previous studies have suggested that there may be various mechanisms contributing to PBDEs toxicity. The present study aimed to outline PBDEs’ toxic effects and mechanisms on different organ systems. Given PBDEs’ bioaccumulation and adverse impacts on human health and other living organisms, we summarize PBDEs’ effects and potential toxicity mechanisms and tend to broaden the horizons to facilitate the design of new prevention strategies for PBDEs-induced toxicity.