Millennial scale variations of terrigenous provenance in marine realm are closely related to regional environment and climate changes. Therefore, a wealth of information of past environment and climate can be constrained via fingerprinting sediment provenance. The Sea of Japan is a unique marginal sea in the North Pacific due to its high sill and distinct thermohaline circulation. The modern hydrography in the Sea of Japan is mainly affected by the East Asian Monsoon and Tsushima Warm Current, one branch of the Kuroshio Current. The Sea of Japan communicates with neighboring seas through four shallow and narrow straits, indicating great effects of global eustatic sea level change on its environment over glacial-interglacial cycles. Here we examine the terrigenous provenance in fine-grained fraction (<63 μm) of core KCES1, located near one end of the Tsushima Strait of the Sea of Japan over the last 48 ka, using radiogenic isotopes of strontium (Sr) and neodymium (Nd). Our data suggest that the terrigenous provenance in core KCES1 was mainly derived from the Yangtze River after 7 ka and a mixture of Yangtze and Yellow Rivers during the last glacial and deglacial periods. Notably, pronounced negative excursions of εNd values at HS1 were attributed to minor additions of unradiogenic Nd contribution from China-Korea cratonic hinterland. A binary mixing model further reveals that >85% terrigenous material is derived from the Yangtze and Yellow Rivers over the last 48 ka. Moreover, abrupt variations in sediment provenance occurred at ~18 ka and ~ 7 ka, which coincide with variations in oceanic surface circulation and deep ventilation recorded in the Sea of Japan. We suggest that paleo-Tsushima Warm Current invaded into the Sea of Japan with reopening of the Tsushima Strait at HS1 and the Tsushima Warm Current substantially entered the Sea of Japan after 7 ka due to intensified Kuroshio Current and rising eustatic sea level. The inflow of Tsushima Warm Current gives rise to a range of changes in surface hydrography, deep ventilation, ecological communities and productivity and sediment texture. The combination of fluxes of paleo-rivers and the intensity of Kuroshio Current, which are closely tied to the eustatic sea level and the East Asian Monsoon, plays a key role in controlling the variations in sediment provenance in the Ulleung Basin. Our study provides unique insight into the tight coupling between changes in sediment provenance and oceanic environment over the last 48 ka in the Sea of Japan.