The increasing production and use of multi-walled carbon nanotubes (MWCNTs) will inevitably lead to discharge into the environment and exert negative effects on organisms. Many studies have focused on the toxicity of MWCNTs to aquatic animals, but little is known about their possible potential reproductive toxicity. In this study, 6 sexually mature Xenopus tropicalis were exposed to 0.5 and 2.5 mg/L MWCNTs suspensions for 56 days, and the toxicity of MWCNTs to the growth and reproduction of X. tropicalis were studied. The results showed that MWCNTs could inhibit the growth of body, including the testis, ovaries and fat of X. tropicalis. Histopathological section analysis showed that MWCNTs affected the formation of spermatogonia and oocytes, while had no notable effect on the heart or liver. MWCNTs would be accumulated in lungs of X. tropicalis inducing lung cannons. In addition, MWCNTs changed the microbial community structure and diversity of gut microbiota but did not change its abundance significantly. Moreover, MWCNTs could even decrease the fertilized and survival rate of X. tropicalis embryos. These results indicated that chronic exposure to MWCNTs would not only affect the growth and development of X. tropicalis, but also pose a potential risk on their reproduction.