ObjectiveTo assess the variability and repeatability of transcranial magnetic stimulation (TMS) target identified by functional connectivity (FC) between the hippocampus and parietal lobes after repeated (multi-run) or a single (one-run) resting-state functional magnetic resonance imaging (fMRI), and to introduce a stable and reliable FC-based target positioning method. MethodsTen runs resting-state fMRI scans were conducted. The FC between the hippocampus and the parietal lobes using each run and the mean FC using multi-run was calculated, respectively. With that, the coordinate of the parietal region with the strongest FC in the aforementioned results was separately set as one- and multi-run targets. The variability and repeatability of the one- and multi-run targets were compared. Finally, five days of rTMS over one- and multi-run targets were performed. Memory tests and Electroencephalography (EEG) was used to assess the effects of rTMS. ResultsThe variability of one- and multi-run targets was 12.96 ± 1.19 mm and 5.33 ± 4.39 mm, respectively. The repeatability of multi-run targets was increased by 22.5 times compared to one-run targets. Compared with one-run targets, rTMS over multi-targets showed more significant results in memory performance, which reduced the event-related potential (ERP) amplitude of the parietal region during memory recollection and improved the FC between the parietal and frontal cortices. We noted significant correlations between changes in memory performance and changes in EEG features. ConclusionStimulation target identified by multiple runs of resting-state fMRI is more stable and reliable than one identified by one run of resting-state fMRI for personalized rTMS.