Repetitive transcranial magnetic stimulation (rTMS) is used to modulate neuronal excitability of the human brain. Distant effects on contralateral corticomotor excitability can be exerted by interhemispheric modulation by low-frequency rTMS on ipsilateral hemisphere. To modulate corticospinal excitability, accurate determination of the stimulation site is important to maximize the effects of rTMS. In the present study, we investigated the difference in the distant effect of 1 Hz rTMS with respect to inducing functional improvement in the non-dominant hand by inhibiting the dominant hemisphere depending on cortical target areas. Ten healthy right-handed volunteers without any neurological disorders were enrolled. The anatomical hand knob (HK) identified from individual magnetic resonance imaging and the transcranial magnetic stimulation (TMS) induced hand motor hotspot (hMHS) by recording motor evoked potentials (MEPs) in the contralateral first dorsal interosseous muscle were determined. All participants underwent three conditions of 1 Hz rTMS on left hemisphere intervention; rTMS application over the HK, rTMS application over the hMHS, and sham-rTMS. Before and after each intervention, all participants undergone motor function assessments with their left hand. The cortical mapping showed that the hMHS was located anteriorly and laterally compared to the HK. Motor function tests showed the most significant improvements after the hMHS stimulation. When we compared the distant effects of target site on corticospinal excitability and motor behavior, delivering 1 Hz rTMS to the hMHS was more effective than delivering it to the HK for improving corticomotor excitability, motor skill, and dexterity. These results suggest that TMS-induced hMHS is an optimal target area to induce distant effect of low-frequency rTMS in motor function.