The composition of the gut microbiota is essential for the host’s health and adaptation to the environment. Due to bacterial functional redundancy in microbial communities, different bacteria can produce the same important metabolites beneficial to health, and studying the gut flora composition of dogs of different breeds under the same domestication conditions can help improve microbial diversity and normalize metabolite production in diseased dogs. In this study, noninvasive sampling and 16S rRNA high-throughput sequencing were used to compare and analyze the structure and function of the gut microbiota of three dog breeds, namely the Chinese Kunming dog (CKD), German Shepherd dog (GSD) and Belgian Malinois dog (BMD). The results showed that the gut microbiota of the three dog breeds consisted of 257 species across 146 genera, 60 families, 35 orders, 15 classes, and 10 phyla. The dominant bacterial phyla across the three breeds were Firmicutes (57.44%), Fusobacteriota (28.86%), and Bacteroidota (7.63%), while the dominant bacterial genera across the three breeds were Peptostreptococcus (21.08%), Fusobacterium (18.50%), Lactobacillus (12.37%), and Cetobacter (10.29%). Further analysis also revealed significant differences in the intestinal flora of the three breeds, at both the phylum and genus levels. The richness of intestinal flora of BMD was significantly higher than that of CKD and GSD. The results of this study provide novel insights into the intestinal flora of intervention dogs and suggest novel methods to improve their health status.