Objective To study the effect of graphene quantum dots (GQDs) on intestinal image formation and mesenteric microcirculation in mice. Methods The effect of GQDs on intestinal image formation was observed using FX-in vivo imaging system in C57BL/6N mice by comparing with X-ray barium meal examination. Pure water was used as negative control and CdTe QDs was used as positive control. The effects of GQDs on the mesenteric arterioles, venules, and capillaries were observed by the mesenteric microcirculation microscope. Results The mouse intestine took on a bright green image under ultraviolet stimulation 1 h after receiving gavage with GQDs, with clear edge and mucosal structure; meanwhile, mesenteric vessels were in clear light green in the mice. High-density images of the small intestine were observed by X-ray in barium meal examination, but the intestinal mucosal structure was not clear, and the mesenteric vessels were not displayed. The diameter of small arteries in GQDs group was greater and that in the barium meal group was smaller than that before gavage. GQDs, CdTe QDs and barium meal had no notable impact on mouse mesenteric venules. The velocities of blood flow in mesenteric arterioles, venules and capillaries were increased after the administration of barium meal or CdTe QDs, and there were no significant changes in GQDs group. Conclusion GQDs is superior to barium meal in image formation of mouse intestinal wall, and it has less influence on mouse mesenteric microcirculation.