Raw milk quality serves as a pivotal determinant throughout the dairy production and processing chain, given that bacterial abundance and diversity exert direct effects on product safety and shelf life. This study employed single-molecule real-time (SMRT) sequencing to profile how production environments shape the microbial community structure of raw camel milk in the Altay and Hami regions of Xinjiang. The dominant phyla across all samples were Firmicutes (43.04%), Proteobacteria (21.98%), Actinobacteriota (16.40%), Bacteroidota (10.61%), and Cyanobacteria (7.91%). Functional profiling revealed that Clusters of Orthologous Groups (COG)-encoded proteins were predominantly enriched in metabolic pathways, particularly amino acid transport and energy conversion. These findings establish a robust scientific foundation for refining raw milk production protocols. Notably, environmental sourcing analysis identified feces and soil as primary reservoirs for key taxa, providing actionable evidence for upgrading quality surveillance systems and optimizing production practices in the camel milk industry.