Deep mantle processes and the dynamic mechanism of magmatism in the Japan Sea Basin are important processes that have not been studied in detail. In this paper, systematic evaluation of basalt samples from the ocean drilling program Site 794 in the Japan Sea was performed, which included petrography, whole-rock major- and trace-element analysis, Sr?Nd?Pb isotopic composition, and electron microprobe analysis of plagioclase and clinopyroxene. These basalts belong to the tholeiitic series with porphyritic texture and massive Ca-rich plagioclase, clinopyroxene, and minor olivine phenocrysts. The basalts are characterized as flat rare earth elements and high-field-strength elements with remarkably low ratios of (La/Yb)N (0.75–2.51), significant positive anomalies of Ba, Sr, and Rb and no Eu anomaly (δEu = 0.99–1.36). The samples showed relatively high 87Sr/86Sr (0.70425–0.70522), 207Pb/204Pb (15.511–15.610), and 208Pb/204Pb (38.064–38.557) values and a low 143Nd/144Nd ratio (0.51271–0.51295). The basalts from Site 794 can be divided into upper, middle, and lower volcanic rocks (UVR, MVR, and LVR) on the basis of their stratigraphic level. The MVR was geochemically derived from the depleted mantle, whereas the UVR and LVR originated from a nondepleted and relatively enriched mantle source with contributions from subducted Pacific plate fluid and sediments. Use of geothermobarometers indicates that the crystallization pressure for the UVR and LVR (6.25–11.19 kbar) was significantly higher than that of the MVR (3.48–5.84 kbar). The UVR and LVR may have been derived from the low-degree (5%–10%) partial melting of spinel lherzolite, while the MVR originated from a shallower mantle source with a high degree (10%–20%) of partial melting. In addition, the geochemical characteristics of the samples are consistent with a younger age (13–17 Ma) and the depleted composition of the MVR and an older age (17–23 Ma) and slightly enriched composition of the UVR and LVR. Therefore, temporal changes in the mantle source from old and enriched to young and depleted and subsequently to old and nondepleted may have been associated with progressive lithospheric extension and thinning, as well as at least two episodes of diverse asthenospheric upwelling and pull-apart tectonic motion in the Yamato Basin.