Chlorothalonil (CTL), an organochloride fungicide applied for decades worldwide, has been found to be present in various matrixes and even accumulates in humans or other mammals through the food chain. Its high residue and diffusion in the environment have severely affected food security and public health. More and more research has considered CTL as a possible toxin to environmental non-target organisms, via influencing multiple systems such as metabolic, developmental, endocrine, genetic, and reproductive pathways. Aquatic organisms and amphibians are the most vulnerable species to CTL exposure, especially during the early period of development. Under experimental conditions, CTL can also have toxic effects on rodents and other non-target organisms. As for humans, CTL exposure is most often reported to be relevant to allergic reactions to the skin and eyes. We hope that this review will improve our understanding of the hazards and risks that CTL poses to non-target organisms and find a strategy for rational use.