Tectonic and climate evolution could be well archived in deep-water stratigraphy. Based on newly acquired high-resolution two-dimensional (2-D) multichannel seismic profiles and multibeam bathymetry, together with Ocean Drilling Program/International Ocean Discovery Program (ODP/IODP) data, this study investigated the late Miocene–Quaternary deep-water seismic stratigraphy, sedimentary evolution, and responses to regional tectonic and climatic variations at the northeastern margin of the South China Sea. The late Miocene–Quaternary stratigraphy consists of three units (i.e., SU-1, SU-2, and SU-3 from bottom to top) that are dated to 10.5–6.5 Ma (stage 1), 6.5–0.9 Ma (stage 2), and 0.9 Ma–present (stage 3), respectively. SU-1 is dominated by sheeted drifts with slight thickness variation, but SU-2 and SU-3 mainly consist of mounded, lenticular contourite drifts and channel-like moats. This suggests that the bottom currents intensified from stage 1 to stage 2, which was probably caused by the sill uplifting at the Luzon Strait under the influence of tectonic collision between the Luzon arc and Eurasia since ca. 6.5 Ma. SU-2 and SU-3 are separated by a basinwide high-amplitude seismic reflection, across which the average sedimentation rate shows a dramatic increase from ~28 m/m.y. in SU-2 to ~144 m/m.y. in SU-3. The high sediment supply since 0.9 Ma could be linked to the mid-Pleistocene climate transition, which resulted in abundant rainfall that promoted the Taiwan orogen to contribute more sediments to the South China Sea. This study indicates that the deep-water stratigraphy recorded the tectonic collision around the sole deep-water gateway (i.e., Luzon Strait) and mid-Pleistocene climate transition event at the northeastern South China Sea margin, which has important implications for understanding the relationships among the tectonic, paleoclimatic, paleoceanographic, and deepwater sedimentary processes in the largest marginal basin of the western Pacific Ocean.