Subclinical mastitis is a critical disease affecting camel health and milk quality. However, research on shifts in milk bacterial communities following subclinical mastitis in camels is limited. We evaluated changes in bacterial communities following subclinical mastitis in Bactrian camels. Three portions of California Mastitis Test (CMT)-negative milk and five portions of CMT-positive milk were collected from each Jimunai County and Keping County using the CMT, and the bacterial community composition of the camel milk was analyzed using amplicon sequencing of the v34 region of the 16S rRNA gene. Subclinical mastitis induced genus-level differences in the core bacterial microbiota of Bactrian camel milk. To our knowledge, was identified in camel milk for the first time, predominantly in Jimunai County. Bacterial abundance in camel milk from Keping County was increased and altered. Alpha diversity analysis revealed that subclinical mastitis induced lower and higher bacterial abundance in milk from Jimunai County and Keping County, respectively, compared to that of healthy camels. Therefore, these findings provide direction for future research on pathogenic microorganisms for the prevention and control of subclinical mastitis in Bactrian camels.