Archaeological records of the Neolithic settlements on the eastern China coast between 35°N and 30°N, an area covering the abandoned Yellow River and the Yangtze River delta plains, reveal that Neolithic people moved from the Yellow River basin onto the northern coast for fishing, hunting and dry-land agriculture ~ 7000 yr ago. Marine transgression interrupted their activities on the low-lying (2–5 m in elevation) coastal wetlands between 6000 and 5000 yr ago, after which they reclaimed their land near the river mouths. Their migration routes on the southern Yangtze delta plain indicate another scenario: early Neolithic communities moved onto the plain for wet-rice cultivation. Despite relative sea-level rise from 7000 to 4000 yr ago, a large number of settlements were established on the lowlands between the eastern Chenier Ridges and the western Taihu Lake depression. The Chenier Ridges, with ~ 1.0 m higher topography than the adjacent coastal area, played a role in sheltering the Neolithic people. Subsequently, settlements waned considerably, possibly due to further marine inundation combined with cold climate. The present study shows that migration patterns of the Neolithic settlements are closely associated with a gradually rising sea level between 7000 and 4000 yr ago.