In recent years, the widespread use of the pesticide cyprodinil has attracted attention due to its harmful effects on aquatic organisms. The purpose of this study was to evaluate the adverse effects of long-term exposure to cyprodinil on the reproductive system of female zebrafish. After the embryos had been treated with 0.1, 1 and 10 μg/L cyprodinil for 180 days, we observed that female fish treated with 1 and 10 μg/L cyprodinil showed decreased sexual attractiveness, a decreased proportion of primordial follicles in the ovary, an increased proportion of mature follicles, and increased egg production. Moreover, exposed females that mated with normal males produced offspring with increased rates of mortality and deformity (the F1 generation). In addition, the levels of gonadotropin and testosterone (T) were increased in females after cyprodinil exposure, especially in the 10 μg/L treated group. After cyprodinil treatment, some key genes in the hypothalamic-pituitary-gonad axis underwent significant changes. For example, gene expression of brain gonadotropin-releasing hormone receptors (gnrhr1, gnrhr2 and gnrhr4) was significantly downregulated after cyprodinil treatment. The study found that expression of the aromatase (cytochrome P450 family 19 subfamily A polypeptide 1a, cyp19a1a) responsible for converting T into estradiol was significantly downregulated after cyprodinil treatment, consistent with elevated T levels in the ovaries and muscles. In summary, these data provide a more comprehensive understanding of the toxicity of cyprodinil and may inform evaluation of the ecotoxicity of cyprodinil to female reproduction at environmentally relevant concentrations.