Camel milk is rich in nutrients and bioactive factors, which are crucial for human nutrition, health, and disease treatment. However, there is limited research on the genes related to lactation traits in Bactrian camels and their regulatory mechanisms. This lack of research prevents the provision of systematic molecular breeding guidance to improve milk production traits and enhance milk quality in Bactrian camels. Previous research has shown a significant difference in milk production traits between the eastern and northern regions of Xinjiang. In this study, 106 Bactrian camels were collected—55 from three camel farms in the northern region and 51 from one farm in the eastern region—for whole-genome resequencing. Through variant detection, population structure, and selection signal analysis, a total of 6,451,453 SNPs were identified. Principal component analysis and phylogenetic tree analysis revealed that the Bactrian camel populations from the eastern and northern regions can be clearly distinguished. GO analysis and KEGG enrichment analysis revealed that, compared to Bactrian camels from the northern region, candidate genes from the eastern region were mainly enriched in two pathways: plasma membrane and thyroid hormone synthesis. Whole-genome selection signal analysis identified eight candidate genes potentially related to lactation traits: DUOX1, DUOX2, CPQ, CGA, PLCG1, FYN, GNRHR, and TRHR. These genes can serve as potential marker sites for molecular breeding in the future.