The physiological and pathological activities between the intestines and other organs influence each other, which comprise various intestinal axes. In cases of inflammatory bowel disease, the gut microbial homeostasis is imbalanced. These gut microbes and metabolites were also able to cross-talk between different organs along the intestinal axis. Although several drugs have been developed for inflammatory bowel disease (IBD) treatment, therapies targeting the intestinal axis still face large limitations. Nanomotors can be actively targeted by external stimuli in different environments or by converting energy sources into self-drive forces, and their inherent initiative and selectivity enable them to overcome the limitation that the passive transportation of traditional drugs is difficult to treat based on the intestinal axis. We reviewed the application of nanomotors in the treatment of IBD, with a focus on exploring the current difficulties and future trends of nanomotor-based therapies targeting the intestinal axis.