The southwestern Ryukyu Trench represents the ultimate sink of sediments shed from Taiwan into the Philippine Sea, which are mainly transported to the trench by turbidity currents via submarine canyons. Here, we present trench turbidites intercalated with hemipelagites in a gravity pilot core and a piston core acquired on the Ryukyu Trench floor at 6147 m water depth. We performed X-ray fluorescence core scans (ITRAX profiles), magnetic measurements, and organic geochemistry analyses to discriminate turbidites from hemipelagites. We identified 36 turbidites (0.9–4.2 cm thick) based on visual core descriptions and Ca/Fe ratios in the ITRAX profiles. Three of these turbidites show magnetic signatures indicating the presence of pyrrhotite and peaks in the magnetic susceptibility profile, suggesting that Taiwan-sourced sediments are transported to the Ryukyu Trench by long-runout turbidity currents. Pyrrhotite is also present in hemipelagites of the upper part of the retrieved cores, indicating a dominant sediment source in Taiwan over the last several thousand years. Ca/Fe and Zr/Rb ratios in the ITRAX profiles mark distal turbidites (about 1–3 cm thick), and Zr/Rb peaks mainly reflect grain size changes. Detailed analyses of a representative turbidite show good correlation between Ca/Fe and Zr/Rb peaks with upward-coarsening and upward-fining trends that delimit the turbidite. Sedimentary organic matter in hemipelagites is characterized by higher total organic carbon and total nitrogen contents and higher δ¹³C values than that in turbidites. Our multi-proxy approach employing high-resolution XRF core scans to differentiate turbidites from hemipelagites contributes to establishing a comprehensive view of modern trench sedimentation from Taiwan to the southwestern Ryukyu Trench.