Objective To explore the effect of repetitive transcranial magnetic stimulation (rTMS) combined with hyperbaric oxygen (HBO) therapy on cognitive function, cerebral blood flow, and negative emotions in patients with traumatic brain injury (TBI). Methods A total of 80 patients with TBI were randomly divided into an experimental group and a control group, with 40 patients in each group. The control group received routine treatment, while the experimental group received rTMS and HBO therapy in addition to routine treatment for a duration of four weeks. Cognitive function (MoCA scores and P300), cerebral blood flow (TCD), and emotional state (HAMA and HAMD scores) were assessed before and after treatment. Results After treatment, all indicators in both groups showed significant improvement (P ＜ 0.05). Compared to the control group, the experimental group demonstrated significantly better improvement in cognitive function (increased MoCA scores, shortened P300 latency, and increased P300 amplitude), cerebral blood flow (increased Vm, Vd, and Vs, decreased PI), and emotional state (lower HAMA and HAMD scores) (P ＜ 0.05). Conclusions rTMS combined with HBO therapy significantly improves cognitive function, cerebral blood flow, and emotional state in patients with traumatic brain injury, outperforming routine treatment alone. This provides a new treatment option for the rehabilitation of TBI patients.