To discuss slip behaviors in shallow slow earthquake regions, we investigate source characteristics of shallow very low frequency earthquakes (VLFEs) southeast off the Kii Peninsula in the Nankai subduction zone. VLFEs are a kind of slow earthquakes and are clearly observed at frequencies below 0.1 Hz. A non-linear inversion technique for moment rate function estimation and the permanent ocean-bottom seismometer network provided us with precise locations and detailed kinematic source characteristics of shallow VLFEs. The high activity of shallow VLFEs around the western edge of the subducted Paleo-Zenisu ridge is similar to previous studies. A notable trend change in the along-dip dependency of shallow VLFE moment rates was found. Along the profile west side of the Paleo-Zenisu ridge, moment rates of shallow VLFEs increase with reaching the megathrust zone. Small-scale topographic fluctuations of the subducted oceanic plate exist along this profile, but large-scale seamount subduction has not been identified even from dense seismic surveys. Similar tendencies have been reported in tectonic tremors in the Nankai and Cascadia subduction zones. On the other hand, the opposite trend appeared along the profile with the Paleo-Zenisu ridge. Small shallow VLFEs were dominant near the summit of the Paleo-Zenisu ridge. Fracture networks or stress fields due to seamount subduction possibly impede large shallow VLFEs around the subducted seamount. Our results suggest that the large-scale heterogeneity of the upper surface of the subducted oceanic plate could control source characteristics of shallow slow earthquakes.