This dataset comprises new data and previously published data on marine lipid biomarkers (brassicasterol, dinosterol, C37 alkenones, and the sum of them [∑PB]) in surface suspended particles at 334 stations from seven cruises between 2010 and 2015, and in surface sediments at 258 stations from eight cruises between 2006 and 2012 in the eastern China marginal seas (ECMS). Of all marine lipid biomarker data, 107 surface suspended particle samples were newly measured, with 227 surface suspended particle samples and 258 sediment samples previously published. We also provide the following oceanographic data, most of which were collected from published results (as described in the publication): sea surface temperature (SST, n = 273, from five cruises in summer of 2010–2015), salinity (n = 273, from five cruises in summer of 2010–2015), nutrient concentrations (dissolved inorganic nitrogen [DIN], dissolved inorganic phosphorus [DIP] and silicate [Si]) (n = 133, from three cruises in summer of 2011 and 2015) and Chl a (chlorophyll a, n = 229, from five cruises in summer of 2010–2014) in the surface water, as well as terrestrial biomarker [∑(C27 + C29 + C31) n-alkanes] contents (n = 226), TOC (total organic carbon content, n = 200), δ13CTOC (stable carbon isotope values for TOC, n=269), and sedimentation rate (n = 220) in surface sediments. Some data were measured using in situ CTD instrument in this study: sea surface temperature and salinity in the East China Sea in June 2010 and July 2013 (n = 54), and Chl a in the Changjiang River Estuary in August 2015 (n = 33). The contents of ∑(C27 + C29 + C31) n-alkanes in the southern Yellow Sea in April 2012 (n = 32) were also newly measured. The surface suspended particle samples were obtained by filtering on Whatman GF/F filters, and the surface sediments were collected by multiple corers or stainless-steel grab samplers. Marine and terrestrial lipid biomarkers were analyzed by gas chromatograph (Agilent 6890N) according to the method in Zhao et al. 2006 (doi: 10.1016/j.orggeochem.2005.08.022) and Wu et al. 2016 (doi: 10.1002/2015JG003167). The study resulting from this analysis has been published in Frontiers in Marine Science (doi:10.3389/fmars.2022.824181).