The Bohai Basin was transformed to an inner shelf sea hundreds of thousands years ago. This youngest land-sea transition participated in the significant modification of the distribution of fresh water, sediment fluxes and climate in East Asia, and played an important role in the origin of the Asian marginal seas. Here we present the results of a magnetostratigraphic investigation and propose a conceptual model for the land-sea transition. Our findings indicate that the transition probably started several million years ago, from a fluvial system during the late Miocene and early Pliocene, to a lacustrine environment between the late Pliocene and Middle Pleistocene, and finally to a marine system in the late Pleistocene. Comparison of our results with previous research suggests that the Bohai Paleolake was initiated from the late Pliocene, was fully developed prior to ~1.0 Ma, and terminated around the late Middle Pleistocene. The Miaodao Islands formed the eastern "barrier" of the basin and since the Pliocene or earlier they played a significant role in blocking the lake water and sediments. They deformed from ~1.0 Ma, subsided significantly at ~0.3 Ma and completely by ~0.1 Ma, resulting in the maturation of the basin as an inner shelf sea.