Select gut microorganisms are gradually being applied to improve the effect of immunotherapy strategies in a variety of diseases, and some good results have been achieved. However, attention should be given to the relationship between the intestinal flora and treatment. In addition, many challenges remain, including how to deal with microbial imbalances and related diseases, especially cancers. The potential regulation and control mechanisms are key topics that need to be studied for future clinical treatment. In this review, we focus on the important role of the gut microbiota in traditional cancer therapy and immunotherapy, and we propose feasible strategies and discuss challenges for targeting the microbiota to prevent tumour progression.