In this study, analysis of mineralogy and geochemistry of fifteen surface sediment samples from four hydrothermal fields in the middle and southern Okinawa Trough is presented. Sediment samples can be divided into two types: (1) Metalliferous group (MS group) containing large amounts of sulfides and sulfate are enriched in Pb, Zn, Cu, Fe, Au, Ag, Ba, As, Hg, Se, Sb, Mo, slightly enriched in U, V, and have rare earth elements (REE) patterns similar to those of hydrothermal vent fluids and sulfides, indicating formation by a complex combination of wasting and erosion primary massive sulfide deposits and plume fallout of sulfides and sulfate. The occurrence of sphalerite with high contents of Fe and of co-existing pyrrhotite as major Fe-sulfide indicate that these minerals are formed at high temperature with low-sulfur fugacity in the Clam and Jade hydrothermal sites. The enrichment of Pb, Zn, Cu, Au, Ag, Ba, As, Hg, Se, Sb, and Mo is related to the presence of galena, sphalerite, Cu-sulfides, stibnite, and realgar in the sediments. (2) Non-metalliferous group (non-MS group) containing small amounts of pyrite are slightly enriched in Pb, Zn, Cu, Au, Ag, As, Hg, Se, Sb, and Mo relative to the East China Sea (ECS) continental shelf sediments, with REE exhibiting a “shale-like flat” patterns and close to Taiwan sediments in a REE discrimination plot, indicating formation by a large amount of terrigenous materials originated from Taiwan Island and a small amount of particles of sulfides in the hydrothermal nonbuoyant plume. The slight enrichment of Pb, Zn, Cu, Au, Ag, As, Hg, Se, Sb, and Mo maybe caused by co-precipitation with the fine-grained sulfides settling from the nonbuoyant plume. The positive relationships between the HREE fractionation index (Gd/Yb)_N, heavy mineral proportion, and δEu suggest that (Gd/Yb)_N can be used as a sensitive indicator for reflecting the effect of hydrothermal activity on the sediments.