This study was conducted to evaluate the effects of glucose, soy oil, or glutamine on jejunal morphology, protein metabolism, and protein expression of the mammalian target of rapamycin complex 1 (mTORC1) signaling pathway in jejunal villus or crypt compartment of piglets. Forty-two 21 d-weaned piglets were randomly allotted to one of the three isocaloric diets formulated with glucose, soy oil, or glutamine for 28 days. On day 14 or 28, the proteins in crypt enterocytes were analyzed with isobaric tags for relative and absolute quantification, and proteins involved in mTORC1 signaling pathway in villus or crypt compartment cells were determined by western blotting. Our results showed no significant differences (P > 0.05) in jejunal morphology among the three treatments on day 14 or 28. The differentially expressed proteins mainly took part in a few network pathways, including antimicrobial or inflammatory response, cell death and survival, digestive system development and function, and carbohydrate metabolism. On day 14 or 28, there were higher protein expression of 4EBP1 in jejunal crypt compartment of piglets supplemented with glucose or glutamine compared with soy oil. On day 28, higher protein expression of p-mTOR in crypt compartment was observed in piglets supplemented with glucose compared with the soy oil. In conclusion, the isocaloric glucose, soy oil, or glutamine did not affect the jejunal morphology of piglets; however, they had different effects on the protein metabolism in crypt compartment. Compared to soy oil, glucose or glutamine may be better energy supplies for enterocytes in jejunal crypt compartment.