The small intestine is the main site for digestion and absorption of nutrients, and the development of the small intestine can be affected by several factors, such as diet composition, age, and genotype. Thus, this study aimed to compare the small intestinal morphology and digestive function differences at different ages of three pig breeds. Thirty litters of newborn Taoyuan black (TB), Xiangcun black (XB), and Duroc (DR) piglets (ten litters per breed) were selected for this study. Ten piglets from each breed were selected and sampled at 1, 10, 21, and 24 d old. The results showed that the TB and XB piglets had lower growth but had higher lactase and maltase activities in the jejunum compared with the DR piglets, while most of the digestive enzyme activities in the ileum were higher in the DR piglets at different ages. The expression levels of nutrient transporters, mainly including amino acids, glucose, and fatty acids transporters, differed in the jejunum at different ages among three pig breeds and were higher in the DR piglets at 1 d old and XB piglets at 24 d old. Collectively, these findings suggest that the phenotypic differences in the growth, intestinal morphology, and digestive function among the three pig breeds mainly resulted from the differences in digestive enzymes and nutrient transporters in the intestine.