Objective: To investigate the effects of repetitive transcranial magnetic stimulation (rTMS) on negative symptoms, cognitive function, brain neurotransmitters, and serum inflammatory factors in patients with schizophrenia. Methods: A total of 110 patients with schizophrenia admitted to Mental Health Center of Shanghai Jiao Tong University School of Medicine from January 2020 to October 2021 were selected and randomly divided into a control group and an observation group according to the random number table method, each group with 55 cases. Both groups maintained the same dose and type of antipsychotic drugs during treatment. The observation group was further given 10 Hz rTMS treatment, and the control group was further given pseudo stimulation. The clinical efficacy, Positive and Negative Syndrome Scale (PANSS) scores, complete cognitive function tests [trail making test (TMT), continuous performance test (CPT-IP), maze test (MAZES), social cognition-emotional management (SC)], brain neurotransmitters [dopamine (DA), glutamate (Glu), gamma-aminobutyric acid (GABA)], serum inflammatory factors [interleukin-6 (IL-6), IL-10, tumor necrosis factor-α (TNF-α), and transforming growth factor-β1 (TFG-β1)] levels were compared between the 2 groups before and after the treatment. Results: The total effective rate of the observation group was significantly higher than that of the control group (89.09% vs 74.55%, P<0.05). Compared with the control group, the negative symptoms, PANSS total score, TMT, CPT-IP, MAZES, and SC scores in the observation group were significantly higher after the treatment (all P<0.05). Compared with the control group, the levels of DA in the brain of the observation group after the treatment were significantly lower, and the levels of Glu and GABA in the brain were significantly higher (P<0.05). After the treatment, the levels of serum IL-6, TNF-α and TFG-β1 in the observation group were lower than those in the control group, while the level of IL-10 was higher (P<0.05). Conclusion: Increased rTMS treatment can significantly improve the clinical efficacy of patients with schizophrenia, effectively improve their negative symptoms, improve cognitive function, correct neurotransmitter disorders in the brain, and regulate inflammatory response.