Thick piles of basaltic lavas named “Graben-Fill Basalt” (GFB) occurring in the Akita-Yamagata basin characterize the magmatism accompanied by the rifting tectonics during the opening of the Japan Sea. These lavas are products of Miocene volcanism during the Daijima-Nishikurosawa (i.e. rifting) stage, when the tectonic setting transformed from continental arc to island arc. Careful and detailed sampling of GFB and adjacent lavas were undertaken from the drilling cores and surface outcrops for radiometric dating and geochemical analysis. The new data obtained from these lavas helped to establish the geochronological and petrogenetic relationship for the volcanic events in the basin, and revealed a transition of magmatic composition, source character, and tectonic setting during rifting. The rifting event of Daijima-Nishikurosawa period in the Akita-Yamagata basin was divided into two stages, i.e., the early rift (before 16.5 Ma) and the syn-rift (16.5-13.5 Ma). The latter was further divided into three, i.e., “early-”, “middle-”, and “late-” syn-rift stages. The early rift stage is characterized by bimodal volcanism of basalts and felsic welded tuffs that erupted into a terrestrial to very shallow marine environment. The basalts are mainly alkaline with enriched Sr isotopic compositions, containing moderately high to high HFSE, and Th/Hf, Th/Yb and La/Yb ratios are variable. The geochemistry of basalts suggests that they derived from heterogeneous lithospheric mantle source, with different degrees of partial melting events. The syn-rift stage is characterized by the formation of a large-scale graben, resulting from pull-apart tectonism. Intense submarine volcanism took place in the bottom of graben, and formed the thick piles of GFB lavas. Distinctive trace element geochemistry was found among lavas of three different sub-stages. Chondrite normalized LREE patterns of GFB with depleted Sr isotopic compositions change from low, to medium, then to medium high values. The ratios of Th/Hf and La/Yb show little variation within each sub-stage, however, the averaged ratios do increase from the early to the late-stage. The compositional change from alkali basalts of early syn-rift stage to tholeiites of middle syn-rift stage suggested the compositional change of the source from depleted to more enriched. Injection of the asthenospheric depleted mantle probably caused the production of the GFB. The variation in trace element composition between different syn-rifting sub-stages also indicates the change of partial melting degree of mantle, from low, to high, then to medium low, which is consistent with the progressive prosper and decline of active rifting in the Akita-Yamagata basin.