Mesenchymal stem cells (MSCs) have drawn great attention because of their therapeutic potential. It has been suggested that intra-venous infused MSCs could migrate the site of injury to help repair the damaged tissue. However, the mechanism for MSC migration is still not clear so far. In this study, we reported that hypoxia increased chemotaxis migration of MSCs. At 4 and 6 hours after culturing in hypoxic (1% oxygen) conditions, the number of migrated MSCs was significantly increased. Meanwhile, hypoxia also increased the expression of HIF-1 alpha and SDF-1. Using small interference RNA, we knocked down the expression of HIF-1 alpha in MSCs to study the role of HIF-1 alpha in hypoxia induced migration. Our data indicated that knocking down the expression of HIF-1 alpha not only abolished the migration of MSCs, but also reduced the expression of SDF-1. Combining the results of migration assay and expression at RNA and protein level, we demonstrated a novel mechanism that controls the increase of MSCs migration. This mechanism involved HIF-1 alpha mediated SDF-1 expression. These findings provide new insight into the role of HIF-1 alpha in the hypoxia induced MSC migration and can be a benefit for the development of MSC-based therapeutics for wound healing.