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To investigate the effect of feeding different diets (non-artificial food and formulated diet and their mix) on specific dynamic action (SDA), digestive capacity and growth performance in carnivorous fish species, we measured the postprandial metabolic response and meal remaining in the stomach, specific growth rate (SGR) and intestinal microbial diversity of juvenile southern catfish (Silurus meridionalis) fed loach meat, formulated diet and their mix at 25 °C. The peak metabolic rate (PMR) and peak metabolic scope (PMS) of both the formulated diet and mixed diet group were higher than those of the loach meat group, and the SDA duration of both the formulated diet and mixed diet groups was shorter than that of the loach meat group. The percentage food remaining in the stomach was the lowest in the formulated diet group and the highest in the loach meat group at 16 and 24 h postfeeding, and the gastric evacuation rate was the highest in the formulated diet group and the lowest in the loach meat group. Both SGR and feeding rate (FR) were the highest in the formulated diet group and the lowest in the loach meat group. The bacterial community richness and relative abundance at the phylum and genus levels in the gut microbiota were higher in most samples of formulated diet group and lower in all samples of the loach meat group. These results indicated that southern catfish fed formulated diet had a higher metabolic response, faster digestion process and better growth performance than those fed loach meat. We suggest that these differences were related to the macronutrient composition (i.e., the relative content of protein, carbohydrate and lipid), type of food, as well as ingredients of formulated diets and gut microbiota.