Repetitive transcranial magnetic stimulation (rTMS) is a promising neuromodulation therapy that facilitates recovery in patients with prolonged disorders of consciousness (pDOC). This study aimed to evaluate the efficacy of dual-target rTMS in treating patients with minimally conscious state (MCS). A total of 20 MCS patients were recruited and randomly assigned to either the real or sham stimulation group. Participants received 10 Hz rTMS targeting the left prefrontal and parietal cortices for 10 consecutive days. The Coma Recovery Scale-Revised (CRS-R) and resting-state EEG were recorded, with relative power spectral density and coherence subsequently computed. Additionally, behavioral assessments were conducted over a six-month follow-up period. Our findings indicate that 10 Hz dual-target rTMS enhances brain oscillatory activity in the frontal, central, and parietal lobes. Specifically, the treatment resulted in a reduction in delta-band activity and an increase in alphaband activity in the frontal lobes, as well as an elevation in alpha-band power in the central and parietal region. In contrast, no significant changes were observed in the sham stimulation group. Meanwhile, in the real stimulation group, long-distance coherence (F3-P4) exhibited increased in alpha-band. These findings suggest that enhanced oscillatory activity and EEG functional connectivity may underlie the modulatory effects of dual-target rTMS. Additionally, a combined prefrontal and parietal cortex approach is another viable option in rTMS protocols for patients with pDOC.