Imazalil (IMZ) is a highly effective fungicide employed in crop production. It has been consistently detected in aquatic environments. The main environmental metabolite of IMZ is imazalil-M (IMZ-M). Limited studies have focused on the toxicity of IMZ and IMZ-M in aquatic organisms. This study systematically evaluated the developmental toxicity of IMZ and IMZ-M on zebrafish (Danio rerio) embryos and explored the potential mechanisms involved. The results showed that IMZ and IMZ-M caused developmental toxicity, characterized by decreased heart rate, hatching inhibition, and pericardial cyst in zebrafish embryos. Subsequently, acridine orange (AO) staining revealed cell apoptosis in the area around the heart regions of zebrafish larvae. Besides, the expression levels of apoptosis-related genes also varied significantly. Furthermore, 1H NMR-based metabolomics analysis showed that IMZ and IMZ-M exposure could induce metabolic profiles disorder in zebrafish larvae. Importantly, zebrafish exposure to IMZ and IMZ-M significantly affected the metabolism of branched - chain amino acids, energy, and ketone bodies, which are related to cell apoptosis. Overall, the toxicity of IMZ and IMZ-M in zebrafish embryos and larvae was characterized, suggesting a theoretical basis for the potential environmental risks of IMZ and its metabolite IMZ-M on non-target organisms.