Since the 19th century, the emergence of model systems has helped researchers further understand cellular signaling pathways, identify potential drug targets, and conduct environmental toxicological studies. Exogenous chemicals, such as pollutants, drugs, and industrial chemicals, may affect brain biological processes and functions and eventually lead to neurological diseases. However, the brain is a complex and well-organized human organ, which is fundamentally different from any existing model system. Animal models may not be able to completely simulate the human brain in testing the neurotoxicity of environmental pollutants due to species differences. Human brain organoids, generated from human pluripotent stem cells, are emerging model systems for neurotoxicological research in line with the real situation of human body at the level of genome, transcriptome, and metabolome, and provide an effective platform for testing neurotoxicity of environmental toxins. We reviewed the latest development of brain organoids technology and its application in the evaluation of environmental neurotoxins, and provided new insights into the application of brain organoids in environmental neurotoxicology.