This dataset provides major element compositions of marine sediments over the past 32 kyr at HydroSed Core MD18-3569 on the Penghu Canyon in the northeastern South China Sea. The data include major element compositions and calibrated CaO* content (CaO associated with silicate fractions of the sample). The samples were collected at 5 cm resolution for the upper 3 m and 2.5 cm resolution for the 3–8 m depth interval at Core MD18-3569 (22°09.30'N, 119°49.24'E; 1320 m water depth) retrieved from the HydroSed cruise aboard the R/V Marion Dufresne in 2018. A total of 364 samples were analyzed at the State Key Laboratory of Marine Geology, Tongji University (Shanghai). Major elements were obtained on pressed pellets of salt-removed bulk samples by X-ray fluorescence (XRF) using a PANalytical Axios spectrometer. Standards of GSD-15, GSD-16, and GSR-6 were used to control the analysis precision with an average deviation of less than ±2% for all major elements. Results of major elements were expressed as their oxides (%) as absolute bulk content of samples.