Sea-level effects on the Kuroshio Current (KC) in the Okinawa Trough (OT) are examined using a 3-D ocean model. When the sea level is -135 m (for the Last Glacial Maximum), topographic high at the southernmost OT partially blocks the KC throughflow, resulting in a 43% reduction of KC inflow. Meanwhile, meandering is enhanced and deepwater ventilation is reduced. However, the KC does not migrate to the east off the OT as suggested previously. When sea level is -40 m (for the beginning of Holocene), the modeled flow pattern resembled present KC in terms of flow path and volume transport. Sea level fluctuation may act as a major control altering the KC course in the OT, leading to significant changes in horizontal and vertical water exchange. It may alter surface water properties, biogeochemistry in both water column and sediments below, potentially, downstream KC and climate over the northeast Asia.