Ionizing radiation not only occurs in radiation terrorist events or nuclear accidents, but also widely exists in clinical practice and daily life. Presently, many studies have focused on the protection of bone marrow and gastrointestinal damage caused by ionizing radiation while there are few studies on its effective protection in male reproductive function damage upon exposure. The normal reproductive function of testis is essential to maintain male lifelong fertility. The location of testis is shallow with high sensitivity to ionizing radiation. Exploring mechanisms of testicular reproductive function damage induced by irradiation are beneficial to develop new countermeasures against radiation injury in testis. Spermatogonial stem cells are the basis for efficient testicular reproductive function. Spermatogonial stem cells develop and grow in the stem cell microenvironment which is composed of Sertoli cells and interstitial cells. Their function is regulated by many factors such as glial cell-derived neurotrophic factor (GDNF) and promyelocytic leukemia zinc finger (PLZF) protein. Ionizing radiation can damage spermatogonia and their microenvironment through DNA damage, oxygen free radicals, different forms of cell death, activation of mammalian rapamycin target complex 1 (mTORC1) and p38 mitogen activated protein kinase (p38 MAPK). Therefore, inhibition of apoptosis, antioxidants, inhibition of mTORC1 and p38 MAPK signal pathways are the existing common protective measures against radiation-induced testicular injury. Polypeptide drugs and spermatogonial stem cell transplantation have good potential in the protection of male reproductive function under ionizing radiation condition. With the in-depth study of the mechanism of male reproductive function damage caused by ionizing radiation, it will be helpful to explore a variety of potential and efficient new ideas for the protection of radiation-induced testicular injury.