Objective To initially explore the possibility of applying the fluorescence micro-optical sectioning tomography (fMOST) high-resolution 3D reconstruction system to the morphological study of the intestinal nervous system and to preliminarily establish a method  for studying the morphology of the intestinal nervous system using this system.    Methods fMOST high-resolution 3D reconstruction system was used to study the intestinal nervous system of C57BL/6 mice in detail. Based on this method, a new morphological method  of the visceral nervous system of small animal models was explored at the single-cell level.   Results Compared with the large intestine, the small intestine lacked the typical myenteric plexus (Auerbach), deep mucosal plexus (Henley), and submucosal superficial plexus (Meissner).   Conclusion The result  of this paper provide a clearer and systematic display of the anatomical structure of the enteric nervous system in C57BL/6 mice, and further clarify the similarities and differences between the enteric nervous system of mice and human, and provide a theoretical basis for its rational application in the study of digestive system diseases. The morphological study of fMOST high-resolution 3D reconstruction system is not limited to the central nervous system, but can be extended to the morphological study of multiple visceral nervous systems.