Human microbiota is composed of bacteria, viruses, fungi and other microorganisms, which are distributed in the oral cavity, nasal cavity, intestine, vagina and skin, etc. Human microbiota plays a pivotal role in the metabolism, immunity, hormones and homeostasis of the host. It can protect the host and maintain the homeostasis, and provoke the incidence of inflammation and tumors. Microbiota has been found to modulate the efficacy and toxicity of chemotherapy and immunotherapy for certain types of tumors. Nevertheless, large-scale studies in the context of radiation therapy have not been performed. In this article, the relationship between the microbiota and the radiotherapy response and toxicity changes of cancer patients was summarized, aiming to develop the optimal treatment plan for patients, and provide evidence for the prevention and treatment of radiotherapy-induced injury.