This data compiles concentrations and compound specific carbon isotope (δ13C) of n-alkanes in 25 surface sediments of Futou Lake in the Yangtze floodplain China. The surface sediments were collected using a Kayak gravity corer and the top 1 cm sediments were sampled in April 2023. Concentrations of n-alkanes were analysed using a Shimadzu GC2010 gas chromatography (GC) equipped with a flame ionization detector (FID) and a DB-5MS column (30 m × 0.25 mm × 0.25 μm film thickness). Compound specific carbon isotope (δ13C) of n-alkanes were analyzed using a Finnigan Trace GC instrument coupled with a Finnigan Delta XP isotope ratio mass spectrometer (GC-IRMS). Both the concentrations and compound specific carbon isotope (δ13C) of n-alkanes were analysed at State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences. Each sample of the compound specific carbo isotopes was analyzed at least twice with peak intensities (m/z 44) > 500 mv and the standard deviation < 0.5‰ were identified as reliable results. Results were reported in the delta notation (‰) relative to Vienna Peedee Belemnite (VPDB).