Aim To observe the effect of cobalt dichloride (CoCl₂) preconditioning on the cerebral infarction volume percentage and the expressions of stroma cell-derived faetor-1α (SDF-1α)/chemokine receptor 4 (CXCR4) in rats; To investigate the protective effect of SDF-1α/CXCR4 biological axis in the brain of the hypoxic ischemic environment. Methods The 168 adult male SD rats were randomly divided into hypoxia preconditioning group (n＝84) and model group (n＝84). According to the time of reperfusion after ischemia, each group was divided into 6 subgroups:6 h, 24 h, 3 d, 5 d, 7 d and 14 d subgroup. The focal cerebral ischemia model was prepared by modified Longa method. The pathological change of brain tissue was observed after hypoxia and ischemia. The change of cerebral infarction volume percentage was observed by triphenyl tetrazolium chloride (TTC) staining after reperfusion in two groups. The expressions of SDF-1α and CXCR4 in cerebral cortex were detected by immunohistochemistry at each time point. Results TTC staining showed that visible infarction focus occured at 6 h and cerebral infarction volume tended to be stable at 24 h in the hypoxia preconditioning group and the model group. There was no significant difference in cerebral infarction volume percentage among 24 h, 3 d, 5 d, 7 d, 14 d in two groups (P＞0.05). Cerebral infarction volume percentage in the hypoxia preconditioning group was significantly less than that in the model group at each time point (P＜0.05). The results of immunohistochemistry showed that the expressions of SDF-1α and CXCR4 increased significantly in the two groups at 6 h, and the expressions were the highest at 7 d, followed by a gradual decrease, and the expression was still in existence at 14 d. The number of SDF-1α and CXCR4 positive cells in the cortex of hypoxia preconditioning group was significantly higher than that in model group (P＜0.05). Conclusion Cobalt dichloride preconditioning can reduce cerebral infarct volume, which may increase the expressions of SDF-1α and CXCR4, induce brain hypoxia tolerance, promote the migration of mesenchymal stem cells to ischemic tissue, and play a protective role in the brain.