Abstract: The Penghu Canyon preserved high-resolution sedimentary records due to its unique deep-sea geographical location and depositional environment, and provided valuable materials for the study of paleoenvironmental evolution. We scanned a drilling core of Well MD18-3570 situated on the west bank of the Penghu Canyon in the northeast of the South China Sea (22°11.48′N, 119°38.68′E, water depth 1572 m, during Sino-French HydroSed cooperation voyage in 2018) at 1-cm resolution using X-ray fluorescence, analyzed the scanning data, and combined with ¹⁴C dating data, from which sediment record evolution and its controlling mechanism since the last 54 ka. Results reveal that the contents of Al, Si, and K were low in the period of 12–30 cal.kaBP and high in other periods, while that of Zr showed the opposite trend to the above three elements. In addition, all the elements showed fluctuations on the centennial-millennial scale. We choose the K/Al ratio to reflect the chemical weathering state of terrigenous detritus, and Si/Al and Zr/Al ratios to reflect the grain-size changes of terrigenous inputs. The K/Al ratio variations were similar to the stalagmite oxygen isotope variations in the Dongge-Hulu Caves, and showed anomalously high values during cold climatic events (the Younger Dryas and Heinrich Events H1–H5), suggesting that the East Asian monsoon precipitation regulated the chemical weathering intensity of the deep-sea sediments. The weakened monsoon rainfall might lead to the reduced chemical weathering and the enhanced physical erosion in Taiwan drainage basin, which is reflected as the increased K/Al ratio (weakened chemical weathering) of the deep-sea sediment records. On the other hand, the enhanced monsoon rainfall induced the opposite sedimentary record. Grain size indicator Zr/Al show high values during the sea-level lowstands (12–30 cal.kaBP), which might be related to the increased coarse-grained input due to shorter transport distances of terrigenous sediments. Therefore, we suggested that sea-level changes regulated coarse-grained terrigenous detritus input, and monsoon rainfall changes regulated the chemical weathering intensity of deep-sea sediments. This study provided the first long-term, high-resolution sedimentary record of the Penghu Canyon, and provided new insights into the evolutionary mechanism of the canyon sedimentary record.