Based upon a high resolution stratigraphic and chronologic framework of core B-3GC in the northern Okinawa Trough during the Holocene, multi-proxies, including a set of marine biomarkers, contents of total organic carbon, opal and CaCO3, are used to reconstruct the past changes of sea surface temperature (SST) and productivity. Evident fluctuations of UK′37-SST and sea surface productivity records could indicate directly the variability of the Kuroshio-Tsushima Current. During 10.6~7.3 ka BP, when the northern Okinawa Trough was dominated by cold coastal water mass from the East China Sea, increasing terrigenous matter input enhanced the primary productivity, whereas the UK′37-SST remained lowering. During 7.3~4.6 ka BP, when the northern Okinawa Trough was abruptly influenced by the Kuroshio Current, the UK′37-SST increased and terrigenous matter input decreased. Although the Kuroshio Current prevented the intrusion from the coastal waters, contents of biomarkers and biogenic components still continuously increased, which was probably caused by the strengthened upwelling in this region. During 4.6~2.7 ka BP (Pulleniatina Minimum Event, PME), the UK′37-SST recorded an evident cooling signal of 0.8~1.4℃, meanwhile, terrigenous matter input, productivity as well as biogenic components all greatly increased. All these changes suggest that the influence of the Kuroshio Current sharply weakened or its main axis may shift to the open Pacific Ocean in this interval. The northern Okinawa Trough was again affected by the coastal waters. During 2.7 ka BP to the present, the Kuroshio Current probably reentered this region, resulting in a warm SST condition. However, primary productivity and biogenic components drastically increased, which may be induced by the persistently enhanced upwelling in the northern Okinawa Trough.