Calorie restriction plays a role in reducing food intake and weight gain, and improving health and lifespan. We hypothesized that calorie restriction would affect body weight (BW), serum indices, gut microbiota, metabolites and short-chain fatty acids of finishing pigs. Castrated male (Landrace × Yorkshire) pigs (86.13 ± 3.50 kg) were randomly assigned into two groups indicated as control (Con) and calorie restriction (CR) (eight pigs/group), respectively. Pigs in the Con group consumed feed ad libitum, whereas pigs in the CR group were fed 70% of the amount of feed in the Con group. The trial lasted for 38 days. Blood and colonic contents were collected for serum parameters, and microbiota and metabolome analysis, respectively. Main effects were tested by Student’s t-test. We found that for finishing pigs, calorie restriction reduced the cumulative food intake, BW gain, serum total cholesterol, triglyceride, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, alanine aminotransferase and aspartate aminotransferase levels. Calorie restriction did not change the α and β diversity of intestinal microbiota. However, calorie restriction significantly increased the abundance of Romboutsia and unclassified_c_Bacilli, and significantly reduced the abundance of Lachnospiraceae_XPB1014_group, Candidatus_Saccharimonas, Escherichia-–Shigella and Gastranaerophilales. Calorie restriction also simultaneously changed the structure of intestinal metabolites and increased the concentration of isobutyric acid, isovaleric acid and valeric acid. In conclusion, calorie restriction may affect metabolism, reduce obesity and improve intestinal microbiota, which may be a healthy diet treatment that can reduce obesity and improve metabolism.