A total of 849 core samples collected from two drilling core STD235 and ZSQD289 in the northeastern South China Sea were analyzed for elemental composition including total organic carbon (TOC), total nitrogen (TN), stable carbon and nitrogen isotopic composition (δ13C, δ15N), and clay mineral composition. Based on clay mineral assemblages and organic geochemistry characteristics, it is supposed that the terrestrial source for sediments at STD235 and ZSQD289 is mainly from southwestern Taiwan. Moreover, the sedimentary organic matter of site ZSQD289 was probably directly inputted from southwestern Taiwan submarine canyon, while the sedimentary organic matter of core STD235 was probably transported by deep water current. The chronology suggested that it covered the record since ~19.7 and 34.6 ka BP in site STD235 and ZSQD289 respectively. Before the Last Glacial Maximum (LGM), high TOC/TN ratios with low δ13C and δ15N values might indicate that terrestrial organic input and nitrogen fixation was enhanced. During the LGM, gradually increased TOC, TN, δ13C, and δ15N values might result from the enhanced burial of organic carbon and higher marine primary production constrained by the strong winter monsoon. TOC/TN ratios and δ13C values generally present a decreased trend from LGM to Holocene (18 - 11 cal ka BP), strongly correlated to the terrestrial organic input and marine primary production reduced during this period. Since Holocene, the terrestrial organic input to both sites further reduced and maintained a low level, in according with a high sea level and a gradual intensified summer monsoon.