In order to explore effective ways to reduce non-suicidal self-injury (NSSI) among female adolescents, a total of 45 female adolescent patients with NSSI in West China Hospital of Sichuan University and Guizhou Second Provincial People's Hospital from June 2021 to June 2024 were selected randomly that divided into groups A, B and C, with 15 cases in each group. Group A was treated with repeated transcranial magnetic stimulation (rTMS) and bipolar depression triple therapy, and group B was treated with bipolar depression triple therapy to compare the effectiveness and safety. Group C received bipolar depression triple therapy combined with sham stimulation which only produced stimulating sounds but no stimulating magnetic field as a control in the study. After treatment, the Hamilton Anxiety Score (HAMA), Hamilton Depression Score (HAMD) and Nurses’ Global Assessment of Suicide Risk (NGASR) in group A were significantly lower than those in group B and C (P < 0.01). rTMS combined with bipolar depression triple therapy has a definite effect on reducing NSSI in female adolescents, which can reduce the incidence rate of short-term NSSI behavior in patients.