To fully understand the bacterial diversity and community structure of goat milk, V3-V4 region of bacterial 16S rRNA gene in metagenomic DNA of goats’ milk samples from Yangling, Baoji and Weinan region of Shaanxi Province were analyzed using high-throughput sequencing. A total of 225424 high-quality sequences were obtained, with an average of 673 OTUs per sample. The analysis of bacterial communities in goat milk from different regions showed that there are 27 bacterial phylum,Proteobacteriadominated the microbiota of all goat milk samples in Guanzhong region of Shaanxi Province, and Weinan area accounted for the greatest proportion with 91.15%, Yangling and Baoji area accounted for 62.44% and 60.33%, respectively. There are 354 bacteria genus, the dominant microorganisms of bacteria were identified asEnterobacter, the proportion in the three areas were 37.41%, 33.82% and 2.87% respectively. At the species level,Pseudomonas aeruginosawere dominant in 826 bacteria species, the proportion in the three areas were 7.96%, 4.34% and 3.20%, respectively, and Weinan area had significantly higher contents ofPseudomonas aeruginosathan Yanglin area and Baoji area. The diversity analysis of bacterial population indicated that bacterial community of goat milk in Yangling and Baoji areas had a higher richness and diversity, while Weinan areas had a lower richness and diversity. The bacteria distribution in diverse goat milk had certain difference, while the gaps in bacterial community structure were smaller, exhibited substantial similarities.