This study aims to compare the therapeutic effects of repetitive transcranial magnetic stimulation (rTMS) and continuous theta-burst stimulation (cTBS) treatment in schizophrenia patients with auditory verbal hallucinations (AVHs). We enrolled 64 schizophrenia patients with AVHs who were treated with either rTMS (n = 32) or cTBS (n = 32), and we compared the clinical outcomes by evaluating parameters from motor evoked potentials, Positive and Negative Syndrome Scale (PANSS), Auditory Hallucination Rating Scale (AHRS), and MATRICS Consensus Cognitive Battery (MCCB), as well as the changes of serum neurotrophic factors before and after the treatment. After the treatment, both treatments resulted in reduced PANSS scores, with the cTBS group showing more substantial symptom improvement across positive, negative, and general symptoms, highlighting the enhanced efficacy of cTBS. Cognitive functions assessed by MCCB also improved in both groups, with cTBS showing a generally higher therapeutic effect. Serum levels of brain-derived neurotrophic factor (BDNF) and glial cell line-derived neurotrophic factor (GDNF) increased following treatment in both groups, with a more notable increase after cTBS, while GABA and glutamate levels remained unchanged. Cardiovascular indices were unaffected by either treatment, suggesting no significant impact on cardiovascular health. Our study found that both rTMS and cTBS treatment can exhibit therapeutic effects in the management of AVHs in patients with schizophrenia. However, cTBS treatment generally shows a higher therapeutic effect than rTMS treatment.