Abstract：Objective：To observe the clinical effect of repetitive transcranial magnetic stimulation （rTMS） in the treatment of disorders of consciousness （DOC） after brain injury. Methods：A total of 130 DOC patients admitted to Wenzhou TCM Hospital of Zhejiang Chinese Medical University from September 2022 to January 2024 were selected and randomly divided into the control group and the observation group by a random number table method，with 65 patients in each group. The control group received conventional treatment，while the observation group was given rTMS treatment on the basis of the control group. Both groups were treated for four weeks. The clinical effects， changes in Coma Recovery Scale-Revised （CRS-R） score， Glasgow Coma Scale （GCS） score， neurotrophic factors， inflammatory factors， cerebral blood flow， blood lipids， vascular endothelial function indexes， and electroencephalogram （EEG） before and after treatment were compared between the two groups. Results：The total effective rate in the observation group was 92.31%（ 60/65），which was significantly higher than 69.23%（ 45/65） of the control group（ P＜0.05）. After treatment， the CRS-R and GCS scores in both groups were significantly increased when compared with those before treatment （P＜0.05），and the above scores in the observation group were significantly higher than those in the control group （P＜0.05）. Compared with before treatment， the serum levels of neuron-specific enolase （NSE） and glial fibrillary acidic protein （GFAP） in both groups were significantly decreased， while the serum level of brain-derived neurotrophic factor （BDNF） was significantly increased after treatment （P＜0.05）；the serum levels of NSE and GFAP in the observation group were significantly lower than those in the control group， and the serum level of BDNF was significantly higher than that in the control group， differences being significant （P＜0.05）. After four weeks of treatment，the serum levels of C-reactive protein（ CRP），tumor necrosis factor-α（ TNF-α），and interleukin-6（ IL-6） in both groups were significantly decreased compared with those before treatment， and the above levels in the observation group were significantly lower than those in the control group， differences being significant （P＜0.05）. After four weeks of treatment， the blood flow velocities of the middle cerebral artery （MCA）， anterior cerebral artery （ACA）， and basilar artery （BA） in both groups were significantly increased compared with those before treatment， and the velocities in the observation group were significantly higher than those in the control group， differences being significant （P＜0.05）. After treatment， the serum levels of total cholesterol （TC）， low-density lipoprotein cholesterol（ LDL-C），and endothelin-1（ ET-1） in both groups were significantly decreased compared with those before treatment，while the serum level of nitric oxide （NO） was significantly increased （P＜0.05）；the levels of TC， LDL-C，and ET-1 in the observation group were significantly lower than those in the control group，and the level of NO was significantly higher than that in the control group， differences being significant （P＜0.05）. Pearson correlation analysis showed that the serum level of ET-1 was negatively correlated with the level of NO in the observation group （P＜0.05）. After treatment， the EEG Young grade in both groups was significantly better than that before treatment， and the EEG Young grade in the observation group was significantly better than that in the control group， differences being significant （P＜0.05）. Conclusion： The rTMS has a good therapeutic effect on DOC after brain injury，which can reduce vascular endothelial function damage，alleviate inflammatory response，lower blood lipids， and improve cerebral blood flow and brain function.