Species in the family Canidae occupy different spatial ecological niches, and some (e.g., wolf) can be kept in zoos. The gut microbiome may differ among various wild and captive canids. Therefore, we compared the gut microbiomes of wild canids (wolf, red fox, and corsac fox) in the Hulun Lake area, captive wolves, and domestic dogs in different regions using metagenomic data. A random forest analysis revealed significant enrichment for bacterial species producing short-chain fatty acids and the thermogenesis pathway (ko04714) in the gut microbiome of wild wolf, potentially providing sufficient energy for adaptation to a wide range of spatial ecological niches. The significantly enriched bacterial species and functional pathways in the gut microbiome of corsac foxes were related to physiological stability and adaptation to arid environments. Alpha diversity of carbohydrate-active enzymes in the gut microbiome was higher in the red fox than in the corsac fox and wild wolf, which may be related to the abundance of plant seeds (containing carbohydrates) in their diets (red foxes inhabit seed-rich willow bosk habitats). However, the influence of host genetic factors cannot be excluded, and further experimental studies are needed to verify the study results. In addition, captive environments drove similarity in carbohydrate-active enzymes (CAZymes) and virulence factors (VFs) in the gut microbiomes of captive wolf and domestic dog, and increased the diversity of CAZymes and VFs in the gut microbiome of captive wolf. Increased VFs diversity may increase the pathogenic potential of the gut microbiome in captive wolves. Therefore, it is necessary to continue monitoring the health status of captive wolves and develop appropriate management strategies.