Beneath the Kii Peninsula, the distribution of low-frequency earthquakes (LFEs) forms three clusters. A previous study shows that one of the clusters has anomalously less amount of cumulative slip than the others. To understand the cause of this variation, we applied a tomographic analysis using arrival times of earthquakes recorded by both ocean bottom seismometers and onshore stations. As a result, we identified segmentation about the Vp/Vs ratio around the subducting plate interface corresponding to the distribution of LFEs. One of the segments has low a Vp/Vs ratio that coincides with the small-slip LFE cluster. Another segment has a high Vp/Vs ratio in which almost no LFEs occur. We conclude that the relatively low pore fluid pressure within the low Vp/Vs segment contributes to the small-slip LFE cluster and that the gap of LFEs within the high Vp/Vs segment corresponds to stable slip area due to high pore fluid pressure.