Objective To investigate the effect of repetitive transcranial magnetic stimulation (rTMS) combined with acupuncture on the restoration of sleep rhythms in patients with insomnia undergoing conventional drug treatment, and evaluate its improvement on sleep quality, sleep structure, and psychological status. Methods A total of 120 insomnia patients receiving conventional drug therapy were randomly divided into three groups: the combined therapy group, the rTMS therapy group, and the acupuncture therapy group, with 40 patients in each group. The combined therapy group received rTMS combined with acupuncture therapy in addition to drug therapy, the rTMS therapy group received only rTMS therapy in addition to drug therapy, and the acupuncture therapy group received only acupuncture therapy in addition to drug therapy. The treatment duration was 4 weeks for all groups. Changes in various indicators before and after treatment were compared and analyzed using the Pittsburgh Sleep Quality Index (PSQI), polysomnography (PSG), Hamilton Depression Rating Scale (HAMD-17), and Hamilton Anxiety Rating Scale (HAMA-14). Results After 4 weeks of treatment, all three groups showed significant improvements in PSQI total scores, PSG-related indicators, HAMD-17 scores, and HAMA-14 scores compared to pre-treatment levels (P<0.05); The combined treatment group showed significantly greater improvements than the two single treatment groups in terms of the reduction in PSQI total scores, shortening of sleep latency, prolongation of total sleep time, reduction in the number of awakenings, and decreases in HAMD-17 and HAMA-14 scores (P<0.05). Conclusion In addition to conventional drug therapy, the combination of rTMS and acupuncture can more effectively restructure the sleep rhythm of insomnia patients, significantly improve sleep quality, alleviate anxiety and depression, and demonstrate superior synergistic effects compared to monotherapy, thereby providing an optimised treatment plan for insomnia