Bone marrow-derived mesenchymal stem cells (BMSCs) from livestock are valuable resources for veterinary therapeutics and animal reproduction. Previous studies have shown that hypoxic conditions were beneficial in maintaining the mesenchymal feature of BMSCs. However, the effects of hypoxia on buffalo BMSCs (bBMSCs) remain unclear. In this study, the effects of hypoxic conditions on cell morphology, migration, polarity, and karyotype of bBMSCs were examined. The results showed that hypoxia (5% oxygen) enhanced colony formation and stress fiber synthesis of bBMSCs. Under the hypoxic culture conditions, the migration capacity and normal karyotype rate of bBMSCs were significantly improved ( p < 0.05), which resulted in weakened cell polarity and enhanced karyotype stability in bBMSCs. In addition, it was significantly ( p < 0.05) upregulated in the expression levels of HIF-TWIST signaling pathway axis-related genes (Hif-1, Hif-2, Twist, Snail, Slug, Fn1, N-cadherin, Collal). The HIF-TWIST axis of bBMSCs was also activated in hypoxia. Finally, it was more effective and easier to maintain the mesenchymal feature of bBMSCs in hypoxic conditions. These findings not only provide theoretical guidance to elucidate the detailed regulation mechanism of hypoxia on mesenchymal nature maintenance of bBMSCs, but also provide positive support to further establish the stable in vitro culture system of bBMSCs.