The ability of the small intestine to perform various functions, such as digestion/absorption of nutrients, gradually declines with age. However, the mechanism that causes intestinal senescence remains unclear. Therefore, age-related changes in the jejunum and ileum were evaluated using senescence-accelerated mouse (SAM) strains that possess characteristic phenotypes of aging. In particular, to understand how senescence affects the small intestine, we investigated whether age-related changes in the morphology of the intestinal villi and its capability to digest/absorb nutrients are associated with the senescence phenotypes identified in specific SAM strains. Four SAM strains were selected (SAMP1, SAMP6, SAMP10, and SAMR1; of which SAMR1 served as a control of SAMP strain) and age-related changes in the small intestine were evaluated for each strain. A villus morphological analysis, mRNA expression level analysis of the small intestine-specific molecules, and disaccharidase activity measurement were performed. We observed that the mRNA expression levels of the genes involved in the differentiation of intestinal epithelial cells and in the digestion/absorption of nutrients were markedly decreased in all the SAM strains, especially in the SAMP10 strain. Our results revealed that all the SAM strains spontaneously induced senescence of the small intestine, which occurred due to the disorders affecting the differentiation/maturation system of intestinal epithelial cells. In addition, it was evident that senile phenotypes, such as brain dysfunction, enhanced intestinal senescence in the SAMP10 strain. The results of this study suggest that the brain-intestinal nervous system may play role in maintenance of villous morphology and nutrients uptake via the GLP-2 and IGF-2 signaling pathway.