Shikoku Basin is unique as being located within a trench-ridge-trench triple junction. Here, we report mineral compositions, major, trace-element, and Sr-Nd-Pb isotopic compositions of bulk-rocks from Sites C0012 (>18.9 Ma) and 1173 (13–15 Ma) of the Shikoku Basin. Samples from Sites C0012 and 1173 are tholeiitic in composition and display relative depletion in light rare earth elements (REEs) and enrichment in heavy REEs, generally similar to normal mid-ocean ridge basalts (N-MORB). Specifically, Site C0012 samples display more pronounced positive anomalies in Rb, Ba, K, Pb and Sr, and negative anomalies in Th, U, Nb, and Ta, as well as negative Nb relative to La and Th. Site 1173 basalts have relatively uniform Sr-Nd-Pb isotopic compositions, close to the end member of depleted mantle, while Site C0012 samples show slightly enriched Sr-Nd-Pb isotopic signature, indicating a possible involvement of enriched mantle 1 (EM1) and EM2 sources, which could be attributed to the metasomatism of the fluids released from the dehydrated subduction slab, but with the little involvement of subducted slab-derived sedimentary component. Additionally, the Shikoku Basin record the formation of the back-arc basin was a mantle conversion process from an island arc to a typical MORB. The formation of the Shikoku Basin is different from that of the adjacent Japan Sea and Parece Vela Basin, mainly in terms of the metasomatized subduction-related components, the nature of mantle source, and partial melting processes.