Resting-state magnetic resonance imaging (RS-fMRI) studies indicated that the repetitive transcranial magnetic stimulation (rTMS) exerts antidepression effect through the functional connectivity (FC) of the DLPFC with the subgenual anterior cingulate cortex (sgACC), pregneual ACC (pgACC), or nucleus accumbens (NAc). It is proposed that the FC-guided individualized precise stimulation on the DLPFC would be more effective. The current study systematically investigated the reliability of the RS-fMRI FC location as well as the FC strength with multiple potential factors. We aimed to provide a stable stimulation target for future FC-guided TMS therapy for affective related disorders. Twenty-one subjects under RS-fMRI conditions with the first two times (V1, V2) scanned on a GE 3 T scanner and the third visit (V3) on a Siemens 3 T scanner. Then the FC strength and location reliability were assessed by using intra-class correlation (ICC) and intra-individual distance, respectively. The factors included deep seed ROIs (midline (mid-) sgACC, left pgACC, mid-pgACC, and left NAc), eyes closed (EC) vs eyes open (EO), frequency bands, FC algorithm (Pearson vs Spearman), scanning length (half a session vs whole session), and location method (FC peak vs center of gravity (COG)). The reliability of the voxel-wise FC strength was low to moderate. The intra-individual distances of the COG were 3.8–7.3 mm across all factors, much smaller than that of FC peak (approximately 30 mm). The COG of seed-based FC might be a potential rTMS stimulation target. Anyway, all potential stimulation targets should be tested in future rTMS treatment studies.