This dataset provides clay mineral assemblages 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 clay mineral assemblages (smectite, illite, chlorite, and kaolinite), illite chemistry index, and illite crystallinity. 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 381 samples were analyzed at the State Key Laboratory of Marine Geology, Tongji University (Shanghai). Clay minerals were identified on oriented mounts of non-calcareous clay-sized (<2 μm) particles by X-ray diffraction (XRD) using a PANalytical X'Pert PRO diffractometer. Replicate analyses of selected samples gave a precision of ±2% (2σ), and the semi-quantitative evaluation of each clay mineral has an accuracy of ~5%.