Diet alters the function and composition of small intestinal epithelial cells, making the relationship between diet and the intestine a focus of much research. This study aimed to clarify the effects of a soft diet on the small intestine. We fed mice a soft pellet diet (SP) and a control hard pellet diet (CD) for 14 days and examined changes in the epithelial cells of the small intestine. We found that the body weights of SP-fed mice were lower than those of CD-fed mice. SP did not alter the length of the small intestine, crypt to villus, or the number of Paneth and Goblet cells, but decreased the expression of small intestinal epithelial cell markers. We also found that SP did not change the copy number of mitochondrial DNA, but decreased the mRNA expression of mitochondrial metabolism genes in SP-fed mice. In addition, we found that E-cadherin, a cell adhesion factor, was decreased in SP-fed mice and that the composition of their microbiota was different from that of CD mice. Our study suggests that SP may impair the homeostasis of small intestine epithelial cells, reinforcing the need for further research on how food texture affects intestinal health.