Short-term slow slip events (S-SSEs) intensively occur at the transition zone along the Nankai subduction zone, southwest Japan. Because crustal deformation due to a single S-SSE is small, the source fault is often represented using a planar uniform single-fault slip model, resulting to little constraint on the spatial heterogeneity in amounts of fault slip. To comprehensively investigate the detailed cumulative spatial distribution of S-SSEs in the entire Nankai subduction zone, we adopted a stacking approach of Global Navigation Satellite System (GNSS) data using low-frequency earthquakes as reference. We extracted cumulative displacements due to a series of S-SSEs from 2004 to 2009; coherent signals in almost opposite direction of plate subduction were obtained. The inverted slip indicated significant slip patches laterally elongated along the transition zone at ~30–35 km depth, and small patches in the shallow portions at ~15–20 km and ~10–15 km depth in eastern Shikoku and in Tokai as well as western Shikoku, respectively. The shallow patches in Shikoku were located on the downdip edge of the coseismic slip area of the 1946 Nankai earthquake, while the Tokai small slip was located on the shallower side of the anticipated source area of a large earthquake. Large slip patches of S-SSEs were complementary to the spatially dense low-frequency earthquake areas; in major S-SSE areas, the number of low-frequency earthquakes is small. This spatial dependence of fault slip style even within the transition zone provides new insights regarding the generation mechanism of slow earthquakes.