The inconsistent flavor of traditionally fermented camel milk (CM) limits its standardization and broader consumer acceptance. A total of 198 lactic acid bacteria (LAB) strains and 120 yeast strains were isolated and identified from traditionally fermented camel milk samples collected in Xinjiang, China. Following taxonomic classification and preliminary screening of the isolates, 39 LAB strains (designated DL1–DL39) and 25 yeast strains (designated DY1–DY25) were selected for further investigation. LAB were first screened for acidification capacity and proteolytic activity, and yeasts were screened for aroma and gas production and acid tolerance; promising strains were then refined by integrating textural properties, E-nose, E-tongue, and sensory evaluation, and their key volatiles were characterized by gas chromatography–mass spectrometry (HS-SPME-GC-MS) combined with relative odor activity values (rOAVs). Two optimal LAB strains, DL19 (Lacticaseibacillus paracasei) and DL29 (Lactiplantibacillus plantarum), and one superior yeast strain, DY3 (Kluyveromyces marxianus), were finally selected. CM fermented by strain DL19 achieved the highest overall sensory acceptability, whereas that fermented by strain DL29 received a significantly higher odor score. HS-SPME-GC-MS analysis identified the compounds responsible for the creamy, buttery, and floral notes in the fermented products, namely 2,4-undecadienal, (2E,4Z)-2,4-decadienal, and δ-nonalactone. DY3 produced the richest odor-active substances, with 2-phenylethanol and γ-undecalactone endowing CM with distinct floral, fruity, and creamy flavors. WGS analysis provided a preliminary assessment of safety-related genomic features of DL19, DL29, and DY3. In conclusion, these indigenous strains show great potential as starter or adjunct cultures for precise flavor regulation of fermented CM. The established multi-index evaluation system effectively supports the standardized production of high-quality fermented CM, facilitating the high-value sustainable utilization of underutilized regional CM resources within the future food supply chain.