Objective To explore the expression of HIF-1α, neuronal apoptosis and the influence of traditional Chinese medicine Sanqi on hematoma after brain injury in rats. Methods Ninety SD rats were divided into 3 groups randomly: blank control group, traumatic brain injury (TBI) group and Sanqi intervention group, and they were decapitated after brain injury at different time points: 6 h, 1 d, 2 d, 3 d, 5 d, 7 d. The model of cerebral hemorrhage was made by autologous non-coagulation in stereotactic locator, the expression of HIF-1α and TUNEL-positive cells (apoptotic cells) in the perihematomal area was detected by immunohistochemistry. Results In blank control group, a small amount of HIF-1α was expressed and apoptotic cells were observed. The expression of HIF-1α was up-regulated in the brain injury group from 6 h, and the apoptotic cells increased in abundance. The peak of HIF-1α was reached at 3 d, then decreased, and remained at the high level on the 7 d. Compared with blank control group, the TBI group was statistically significant (P < 0.05). The Chinese medicine Sanqi intervention group significantly up-regulated HIF-1α’expression and decreased neuronal apoptosis, which was statistically significant (P < 0.05). Conclusion HIF-1α’s expression was up-regulated around the hematoma after brain injury, and the apoptosis of nerve cells was obviously increased. The traditional Chinese medicine Sanqi can significantly increase the expression of HIF-1α, reduce the apoptosis around the hematoma, and thus play a neuroprotective role.