Increasing evidence shows that long-term exposure to non-ionizing radiation (NIR) is a risk factor for cancer, male infertility and other diseases. Current studies have revealed the adverse effects of NIR on sperm parameters and on the role of kinases in germ cell metabolism and endocrine system, and can lead to genotoxicity, genomic instability and oxidative stress. However, the biological and molecular mechanisms of infertility caused by NIR on male reproductive organs are still not clear. The purpose of this review is to summarize the current biomedical research on the mechanism of male infertility caused by NIR, discuss the effects of NIR on reproductive endocrine system, sperm kinase activity and redox balance, as well as apoptosis, DNA damage and epigenetic changes induced by NIR, and look into the future research in this field.