The research on the enantioselective toxic effects of chiral pesticides on non‐target aquatic organisms has attracted more and more attention. This study investigated the enantioselective toxic effects of mefentrifluconazole (MFZ) on acute toxicity, developmental toxicity, locomotor behaviors, and the mRNA relative expression levels of genes related to neurodevelopment and cardiac development in zebrafish embryos or larvae. The 96‐h lethal concentration 50 (LC50) values (exposed to racemate and enantiomers of MFZ, that is, rac‐MFZ/(−)‐MFZ/(+)‐MFZ) were 1.010, 1.552, and 0.753 mg/L for embryo, and 0.753, 1.187, and 0.553 mg/L for larvae. The rac‐MFZ/(−)‐MFZ/(+)‐MFZ can affect the heart development of zebrafish embryos, accompanied by heart rate inhibition, yolk sac deformities, pericardial deformities, and down‐regulation of genes related to cardiotoxicity in larvae in an enantioselective manner. Moreover, the rac‐MFZ/(−)‐MFZ/(+)‐MFZ also can affect the neural development of zebrafish embryos, accompanied by autonomic movement inhibition, swimming speed and swimming distance abnormalities, and down‐regulation of genes related to neurotoxicity in larvae in an enantioselective manner. For all toxicity endpoints, the effect of the (+)‐MFZ to early‐staged zebrafish were significantly greater than that of (−)‐MFZ. These results will help distinguishing the difference of MFZ enantiomers to zebrafish, and provide scientific reference for improving the risk assessment of chiral pesticides MFZ.