The Nankai Trough subduction zone is a typical subduction system characterized by subduction of multiple geological units of the Philippine Sea Plate (the Kyushu-Palau Ridge, the Shikoku Basin, the Kinan Seamount Chain, and the Izu-Bonin Arc) beneath the Eurasian Plate in the southwest of Japan. This study presents a geophysical and geochemical analysis of the Nankai Trough subduction zone in order to determine the features and subduction effects of each geological unit. The results show that the Nankai Trough is characterized by low-gravity anomalies (−20 mGal to −40 mGal) and high heat flow (60–200 mW/m2) in the middle part and low heat flow (20–80 mW/m2) in the western and eastern parts. The crust of the subducting plate is 5–20 km thick. The mantle composition of the subducting plate is progressively depleted from west to east. Subduction of aseismic ridges (e.g., the Kyushu-Palau Ridge, the Kinan Seamount Chain, and the Zenisu Ridge) is a common process that leads to a series of subduction effects at the Nankai Trough. Firstly, aseismic ridge or seamount chain subduction may deform the overriding plate, resulting in irregular concave topography along the front edge of the accretionary wedge. Secondly, it may have served as a seismic barrier inhibiting rupture propagation in the 1944 Mw 8.1 and 1946 Mw 8.3 earthquakes. In addition, subduction of the Kyushu-Palau Ridge and hot and young Shikoku Basin lithosphere may induce slab melting, resulting in adakitic magmatism and the provision of ore-forming metals for the formation of porphyry copper and gold deposits in the overriding Japan Arc. Based on comparisons of their geophysical and geochemical characteristics, we suggest that, although the Izu-Bonin Arc has already collided with the Japan Arc, the Kyushu-Palau Ridge, which represents a remnant arc of the Izu-Bonin Arc, is still at the subduction stage characterized by a single-vergence system and a topographic boundary with the Japan Arc.