Holocene geomorphic changes have fundamentally shaped the spatial-temporal distributions of prehistoric and historical settlements in North China. Through intensive field surveys and careful field examination of typical sedimentary sequences, we reconstructed the Late-Pleistocene and Holocene geomorphic history in the two major basins of the mid-lower Fen River, central-south Shanxi, China. Our first-hand data provides crucial information for reconstructing the dynamic relationship between the characteristics of Holocene geomorphic changes and settlement distribution patterns in the two basins from the Neolithic period to the Bronze-Age Xia-Shang Dynasties. In the Taiyuan Basin, due to river downcutting processes from the end of the Late Pleistocene to the Early Holocene, edge of the basin emerged and evolved into tablelands. The elevation of the flat lands atop the tablelands that was significantly above the level of floodwater provided an ideal environment for early settlements. The Holocene geomorphic changes are characterised by continous fluvio-lacustrine aggradation, and the central basin became void of human settlements due to uninhabitable hydrological and gemorphic conditions and especially due to frequent floods. Instead, most settlements were located along the basin, displaying a unique "around-basin" distribution pattern. In the Linfen Basin, following large-scale incision of the main channels and branches of the Fen River during the Late Pleistocene, platform-type plain with deep incised valleys was formed. Similar to the surrounding loess tableland, the central basin became an optimal environment for human activities and settlement construction, forming a "full-basin" like settlement distribution pattern that is distinctively different from the "around-basin" distribution pattern in the Taiyuan basin.