This dataset includes total organic carbon (TOC), stable carbon isotope (δ13C), and radiocarbon activity (expressed as Fm) of TOC, as well as mineral surface area (SA), mean grain size, and calcium carbonate (CaCO3) of 89 surface sediment samples from the northern South China Sea. The samples were collected through the German R/V SONNE cruises SO50, SO72A, SO95, and SO132 during July–September 1987, October–November 1990, April–June 1994, and June–July 1998, respectively. TOC and stable carbon isotope (δ13C) of the decarbonated samples were measured by an elemental analyzer interfaced with an isotope ratio mass spectrometer (EA-IRMS; Flash EA 1112 HT-Delta V Advantage). The standard deviations of TOC content and δ13C were 0.03% and 0.08‰, respectively, by replicate measurements of the same acetanilide standard samples. Radiocarbon activity of carbonate free sediment were measured using a Mini Carbon Dating System (MICADAS) accelerated mass spectrometry at the Laboratory of Ion Beam Physics, ETH Zürich. Radiocarbon data are reported as "fraction modern" (Fm), representing the deviations of the 14C/12C ratio from 95% modern oxalic acid standard. The absolute error of Fm is better than ±0.01. The conventional radiocarbon ages are calculated based on the equation of t = –8033 ln (Fm), in years Before Present (yr BP, where present is 1950 AD). Organic-free mineral surface area (SA) was measured using a 5-point Brunauer-Emmett-Teller (BET) nitrogen adsorption method on NOVA 4000 SA analyzer (Quantachrome Instrument). The standard deviations of two reference minerals are 0.03 and 0.14 m2 g–1, respectively. The sample was then performed for mean grain size analysis using a laser Particle Size Analyzer (Malvern Mastersizer 2000). The calcium carbonate content of the samples was determined by a vacuum-gasometric system with a relative accuracy of ±0.7%.