The Kuroshio Current (KC) is the northward branch of the North Pacific subtropical gyre (NPG) and exerts influence on the exchange of physical, chemical, and biological properties of downstream regions in the Pacific Ocean. Resolving long-term changes in the flow of the KC water masses is, therefore, crucial for advancing our understanding of the Pacific's role in global ocean and climate variability. Here, we reconstruct changes in KC dynamics over the past 20 ka based on grain-size spectra, clay mineral, and Sr–Nd isotope constraints of sediments from the northern Okinawa Trough. Combined with published sediment records surrounding the NPG, we suggest that the KC remained in the Okinawa Trough throughout the Last Glacial Maximum. Together with Earth-System-Model simulations, our results additionally indicate that KC intensified considerably during the early Holocene (EH). The synchronous establishment of the KC “water barrier” and the modern circulation pattern during the EH highstand shaped the sediment transport patterns. This is ascribed to the precession-induced increase in the occurrence of La Niña-like state and the strength of the East Asian summer monsoon. The synchronicity of the shifts in the intensity of the KC, Kuroshio extension, and El Niño/La Niña-Southern Oscillation (ENSO) variability may further indicate that the western branch of the NPG has been subject to basin-scale changes in wind stress curl over the North Pacific in response to low-latitude insolation. Superimposed on this long-term trend are high-amplitude, large century, and millennial-scale variations during last 5 ka, which are ascribed to the advent of modern ENSO when the equatorial oceans experienced stronger insolation during the boreal winter.