Using protein-restriction diets become a potential strategy to save the dietary protein resources. However the mechanism of low-protein diets influencing pigs’ growth performance is still controversial. This study aimed to investigate the effect of protein-restriction diets on gastrointestinal physiology and gut microbiota in pigs. Eighteen weaned piglets were randomly allocated to three groups with different dietary protein level. After a 16-week trial, the results showed that feeding an low-protein diet to pigs impairs epithelial morphology of duodenum and jejunum (p < 0.05), reduces the concentration of many plasma hormones (p < 0.05), such as ghrelin, somatostatin, glucose-dependent insulin-tropic polypeptide, leptin and gastrin. The relative abundance of Streptococcus and Lactobacillus in colon and microbiota metabolites are also decreased by extremely protein-restriction diets (p > 0.05). These findings suggest that long-term ingestion of a protein-restricted diet could impair intestinal morphology, suppress gut hormone secretion, and change the microbial community and fermentation metabolites in pigs, while the MP diet had minimal effect on gut function and did not impair growth performance.