Numerous studies have shown that fluoride exposure adversely affected the male reproductive function, while the molecular mechanism is not clear. The present study was to investigate the effects of fluoride exposure (60days) on the expressions of reproductive related genes, serum sex hormone levels and structures of the hypothalamus-pituitary-testicular axis (HPTA), which plays a vital role in regulating the spermatogenesis in male mice. In this study, 48 male mice were administrated with 0, 25, 50, and 100mg/L NaF through drinking water. Results showed that the malformation ratio of sperm was significantly increased (P<0.05). At transcriptional level, the expression levels of follicle-stimulating hormone receptor (FSHR), luteinizing hormone receptor (LHR), inhibin alpha (INH?), inhibin beta-B (INH?B), and sex hormone binding globulin (SHBG) mRNA in testis were significantly decreased (P<0.05). Moreover, histological lesions in testis and ultrastructural alterations in hypothalamus, pituitary and testis were obvious. However, the same fluoride exposure did not lead to significant changes of related mRNA expressions in hypothalamus and pituitary (P>0.05). Also, there were no marked changes in serum hormones. Taken together, we conclude that the mechanism of HPTA dysfunction is mainly elucidated through affecting testes, and its effect on hypothalamus and pituitary was secondary at exposure for 60days.