The aroma of camel milk is a key sensory indicator for evaluating its quality and flavor. Camel milk collected at different lactation stages exhibits unique flavor characteristics. However, no systematic study has yet explored the aroma characteristics and variation patterns of camel milk across these stages. This study employs HS-SPME-GC-MS, multivariate statistical analysis, and metagenomics to systematically reveal differences in aroma formation in camel milk across lactation periods and their interactions with microbial communities. A total of 577 metabolites is detected. Through OPLS-DA screening, 24 key differential flavor compounds are identified. ROAV analysis indicates that 2,4-undecadienal and (E)-2-undecenal are the main contributors to the fatty, creamy, fresh green, and citrus aromas of camel milk. Some compounds are more abundant in colostrum, while others are richer in mature milk. For microbiota, colostrum is dominated by Proteobacteria, Psychrobacter, and Janthinobacterium, whereas mature milk is dominated by Acinetobacter and Moraxella. Mature milk shows significantly higher alpha diversity and species richness. Spearman correlation analysis shows that core bacterial groups such as Enterococcus and Lactococcus are significantly positively correlated with characteristic flavor compounds, including aldehydes and lactones. This finding suggests that HS-SPME-GC-MS, combined with multivariate analysis, effectively distinguishes patterns associated with microbes and flavor metabolites in camel milk at different lactation stages, which provides a theoretical basis for quality control and further processing of camel milk.