Objective The aim of this study was to observe and analyze the differences of reproductive system in fertile and infertile male naked mole rats. Methods Five fertile and 5 infertile 2-5-year old male naked mole rats were used in this study. The testis and epididymis on one side were collected, weighted, and measured to get their viscera coefficient. The other side testicle was collected and fixed in neutral formalin solution for histological examination.The other side epididymis was used to examine the sperm count and sperm activity. Serum of the naked mole rats was collected to measure the level of luteinizing hormone (LH) and testosterone (T). Results Compared with the fertile group, the testis weight of infertile group was significantly decreased (P < 0.05), their epididymis weight, testicular coefficient and the epididymis coefficient were all significantly decreased (P < 0.01), all their sperm count and sperm activity and their LH and T levels were significantly decreased (P < 0.01 for all). Pathological examination of the testicular tissues of the fertile group showed that many types of spermatogenic cells were seriously detached, the numbers of Sertoli cells and stromal cells were decreased. Mature sperms in the seminiferous tubules were highly decreased in number or even completely disappeared. Conclusions Compared with the fertile individuals, the reproductive system of infertile male naked mole rats presents structural atrophy and declined function.