The present study was designed to investigate the microscopic features of the small intestine in the southern white-breasted hedgehog (Erinaceus concolor). The histochemical profile of the small intestine was investigated using periodic acid Schiff (PAS), alcian blue (AB, pH 2.5), and aldehyde fuchsin. The expression of SOX9 was also evaluated immunohistochemically, and the detailed morphology of intestinal mucosa was studied by using a scanning electron microscope. The intestinal wall was composed of the tunica mucosa, tunica submucosa, tunica muscularis, and tunica serosa. Plica circulares and muscularis mucosa were present only in the duodenum. The jejunal villi were the tallest and the ileal villi were the shortest. From the duodenum to the ileum, the population density of goblet cells decreased significantly. The goblet cells throughout the small intestine reacted positively with PAS and AB. The expression rate of SOX9 was not statistically different between the three parts of the small intestine (p > 0.05). In conclusion, despite the general characteristics of the small intestine in this species of hedgehog, there were some differences when compared with other mammalian and rodent species. These findings provide a baseline for future detailed research on the digestive system of the hedgehog species and other mammalian species.