Abstract The study investigated the effects of carbohydrate-active enzymes and protease complex on growth performance, meat quality, toxic gas emissions, and the structure and functions of colonic microbiota under two protein levels. Duroc × (Landrace × Yorkshire; n = 200) finishing pigs (68.03, SD = 3.57 kg) were allocated to 1 of 4 treatments and received different diets including high protein (16.73%, HP) with/without 0.1% multi-enzymes (ENZs) and medium-high protein (14.73%, MP) with/without 0.1% ENZs, using a 2 × 2 factorial arrangement. The trial was carried out for 7 weeks. The results indicated that ENZs supplementation increased average daily gain (ADG, P < 0.05) probably resulted from an improved apparent total tract digestibility of dry matter and gross energy. The HP diet promoted augmented ADG during the overall period. The MP-treated pigs had greater marbling and intramuscular fat in the longissimus dorsi muscle (P < 0.01). As expected, The HP groups released more ammonia and hydrogen sulfide in the excretion (P < 0.05). The HP improved α-diversity, as revealed by greater observed_ ASVs and Chao1 (P < 0.05) and boosted greater abundance of Firmicutes, Desulfobacterota, Verrucomicrobiota, and Fibrobacterota than the MP diet. The interactive effect of HP and ENZs showed greater Shannon and Pielou's evenness (P < 0.05) with greater Bacteroidota and decreased Firmicutes abundance. Dietary ENZs increased the abundance of Actinobacteriota, Desulfobacterota, and Lactobacillus and reduced pathogenic Clostridium_sensu_stricto_1. Spearman’s correlation indicated that greater acetate concentration in colonic digesta was positively associated with Lactobacillus, Muribaculaceae, Rikenellaceae_RC9_gut_group, Oscillospiraceae-NK4A214_group, Ruminococcus, [Eubacterium]_coprostanoligenes_group at the genus level. Taken together, HP or ENZs supplements improved the ADG and nutrient digestibility of finishing pigs. The interactive effects of CP levels and ENZs supplements did not show the growth performance but the effect of HP with ENZs promoted microbial diversity and stability in the colon.