The South Yellow Sea (SYS) Basin, which is part of the West Pacific Continental Margin, began to form in the late Mesozoic to early Cenozoic as a result of regional tectonic activity in Asia. The pre-Middle Pleistocene sedimentary history of the area remains poorly understood or controversial, mainly due to a lack of long borehole cores penetrating pre-Quaternary strata. Borehole core CSDP-1 (300.10 m long), the longest sediment core recovered thus far from the SYS, was drilled in 2013 in the western SYS. Recently, a reliable timescale for the core for the last similar to 3.50 Myr was obtained by magnetostratigraphy (Liu et al., 2016a). Here we report the results of integrated analyses of the core, including sedimentary characteristics, downcore changes in environmental proxies (benthic foraminifera and ostracods), and accelerator mass spectrometry C-14 and optically stimulated luminescence dates. In addition, we analyze 546 km of single-channel seismic profiles and similar to 50 km of a boomer seismic profile around the core site, and correlate the regional stratigraphy. The core sedimentary succession contains 17 depositional units (lithofacies associations) corresponding to three major seismic units, reflecting a variety of depositional environments during the last similar to 3.50 Myr. Our results show that fluvial environments prevailed in the western SYS from 3.50 to 1.66 Ma, followed by alternations of tidal-flat to shallow-subtidal environments with fluvial environments from similar to 1.66 to 0.83 Ma, and alternations of modern-like marine environments and fluvial environments from similar to 0.83 Ma to the present-day in response to glacio-eustatic sea-level cycles. The depositional succession during the last similar to 3.50 Myr was dominantly controlled by tectonism and glacio-eustatic sea-level cycles. The presumed first marine transgression since the Neogene in the western SYS at similar to 1.66 Ma is interpreted to suggest that sea water could partially flood the Zhe-Min Uplift (ZMU) into the SYS due to tectonic subsidence, and further subsidence of the ZMU and the SYS shelf is inferred to have resulted in establishment of normal marine environments in the SYS during the highstands of glacio-eustatic sea-level cycles since similar to 0.83 Ma. The average subsidence rates in the western SYS were similar to 120-165 m/Myr during the last similar to 1.66 Myr. The sedimentary succession comprises fifth- and fourth-order sequences, which are interpreted to have been driven by the 20-kyr or 41-kyr and by the 100-kyr glacio-eustatic sea-level cycles, respectively, since the late Pliocene. The sequences deposited since the Late Pleistocene are relatively complete, recording deposits from MIS 5 to MIS 1. However, the pre-Upper Pleistocene sequences show significant stratigraphic hiatuses, presumably caused by fluvial erosion during the glacial sea-level lowstands and subsequent transgressive erosion. This type of significant discontinuity in the sedimentary record can be considered to be diagnostic of shelf sequences controlled by glacio-eustatic sea-level cycles.