Environmental pollutants are mainly produced by human production and living, and pose a serious threat to human health. Health risk assessments of environmental pollutants are needed in order to contribute to the development of reasonable control measures. In comparison to two-dimensional (2D) cell culture and experimental animals, organoids are excellent alternative models for health risk assessment of environmental pollutants. In this review, we described the development and application of organoids in models for the toxicity testing of environmental pollutants. Finally, there was a discussion of the unique advantages and challenges of organoids as toxicity test models. It is hoped that this will provide a unique insight into the application of organoids in the field of toxicology.