Asian marginal seas play an important role in moderating material and energy flux linkages between Asia and the Northwest Pacific, and thus have profound climatic and environmental effects. In this study, by combining paleomagnetic study with sediment grain-size analysis on the Lz908 borehole sedimentary sequence from the southern Bohai Sea, new insights into regional geomorphological process since the late early Pleistocene are obtained. The main results are as follows. (1) Paleomagnetic findings suggest that the sequence recorded the Brunhes normal chron and the late Matuyama reverse chron, including the Jaramillo normal subchron. (2) The sedimentary processes in the study area since 1327 ka show a three-stage pattern, with depositional rates of 4.3, 17 and 107 cm/ka during 1327–260 ka (later part of the early and middle Pleistocene), 260–10 ka (late middle and late Pleistocene), and the Holocene, respectively. (3) The sedimentary basin was a part of the Bohai Paleolakes (BHPL) prior to 260 ka, whose water levels were consistently higher than 3 m above the present-day level. After 260 ka, seawater entered the Bohai basin, and relative sea level cyclically fluctuated with global sea-level changes. We therefore infer that the Miaodao Islands, which were the natural barrier of the BHPL blocking seawater entry, had partially subsided before 260 ka, only allowing seawater to enter the basin during a global sea-level maximum. The BHPL terminated around 260 ka, and the “barrier” subsided completely around ~ 130 ka, causing the Bohai basin to become an inner shelf sea.