Abstract: 【Objective】To explore the therapeutic efficacy of intermittent theta burst stimulation (iTBS) on social cognitive function and metabolic syndrome (Mets) of schizophrenia patients with comorbid Mets.【Methods】A total of 80 schizophrenia patients with comorbid Mets were randomly assigned at the ratio of 1 to1 to experimental group or control group. The experimental group received 20 sessions of iTBS treatment for 4 weeks while the control group received sham stimulation. Assessments were conducted at baseline, the second week, and the fourth week after treatment using the Chinese facial emotion recognition test (CFERT) and the Hinting Task (HT); in addition, High density Lipoprotein Cholesterol (HDL-C), Low density Lipoprotein Cholesterol (LDL-C), Triglyceride (TG), Fasting Insulin(FINS) were measured.【Results】A total of 36 participants in the experimental group and a total of 39 in the control group completed the trial. There was no statistic difference in demographic data, scale scores, or metabolic indicators between the two groups at the baseline (P>0.05). After treatment, the levels of CFERT scores, anger, fear, sadness, surprise; HT scores, HDL-C, LDL-C, and TG (all P< 0.05) in the experiment group were significantly different from thos of the baseline and those of the control group. Side effects did not differ between the two groups (P=0.627). There no corelation between social cognition and metabolic marks.【Conclusion】iTBS can effectively ameliorate social cognition and metabolic marks of schizophrenia patients with comorbid Mets. However, it may also cause adverse reactions such as headache and finger spasms.