The small intestine is the major site of animal digestion and absorption; however, little is known about the morphological characteristics of the hedgehog’s small intestine. This study was conducted to investigate the microstructure of the hedgehog’s small intestine and mast cell distribution by conventional HE and modified toluidine blue staining, respectively. Despite its similarity to the general mammal small intestine microstructure, the present results indicated that the hedgehog duodenum contained fewer Brunner’s glands, and that the Paneth cells were lacking in the crypt. The connective tissue was denser in the jejunal submucosa, but the muscularis was thicker. The intestinal glands were greatly developed in the ileum, lymphoid nodules were observed in the mucosa, and diffuse lymphoid tissue was distributed in the lamina propria. Meanwhile, goblet cells gradually increased from the duodenum to the ileum. The mast cells showed various shapes and sizes in the small intestine and could be detected at four layered structures in the small intestine, but were mainly distributed in the lamina propria and the submucosa, surrounded with connective tissue and blood vessels. In conclusion, the mast cells, goblet cells, lymphocytes and lymphoid nodules contributed to the small intestine mucosal immune barrier, and the distribution characteristics of the mast cells demonstrated great significance for the hedgehog’s immune system.